From d0cb7f08c00440a86764907e995f32365469d5d1 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 4 May 2018 13:24:37 +0200
Subject: [PATCH 01/75] R6 import added

---
 DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 53c6f7a..e72ca3b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -47,6 +47,7 @@ Imports: shiny,
     shinycssloaders,
     log4r,
     openssl,
-    methods
+    methods,
+    R6
 RoxygenNote: 6.0.1
 biocViews:

From b259f97696292051bc2f75a787453e2d3fe9f229 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 4 May 2018 13:25:18 +0200
Subject: [PATCH 02/75] implemented Clarion class

---
 NAMESPACE      |   1 +
 R/clarion.R    | 190 +++++++++++++++++++++++++++++++++++++++++++++++++
 man/Clarion.Rd |  32 +++++++++
 3 files changed, 223 insertions(+)
 create mode 100644 R/clarion.R
 create mode 100644 man/Clarion.Rd

diff --git a/NAMESPACE b/NAMESPACE
index dac65a7..32c24b5 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(Clarion)
 export(and)
 export(andUI)
 export(colorPicker)
diff --git a/R/clarion.R b/R/clarion.R
new file mode 100644
index 0000000..cedc7a9
--- /dev/null
+++ b/R/clarion.R
@@ -0,0 +1,190 @@
+#' Clarion R6-class definition
+#'
+#' Use this to create a clarion object.
+#' This object is used by all top-level wilson modules.
+#'
+#' @param header A named list. Defaults to NULL.
+#' @param metadata Clarion metadata in form of a data.table.
+#' @param data Data.table according to metadata.
+#' @param validate Logical value to validate on initialization. Defaults to TRUE.
+#'
+#' @examples
+#' # initializing a new object
+#' object <- Clarion$new(header, metadata, data, validate = TRUE)
+#'
+#' # create a deep copy
+#' object_copy <- object$clone(deep = TRUE)
+#'
+#' @export
+Clarion <- R6::R6Class("Clarion",
+                       public = list(
+                         header = NULL,
+                         metadata = NULL,
+                         data = NULL,
+                         get_uniqueID = function() {
+                           # return unique_id
+                           # if no type return first feature
+                           if (is.element("type", names(self$metadata))) {
+                             return(self$metadata[type == "unique_id"][["key"]])
+                           } else {
+                             return(self$metadata[level == "feature"][["key"]][1])
+                           }
+                         },
+                         get_name = function() {
+                           # return name
+                           # if not existing fall back to unqiue_id
+                           if (is.element("type", names(self$metadata)) && is.element("name", self$metadata[["type"]])) {
+                             return(self$metadata[type == "name"][["key"]])
+                           }
+                           return(self$get_uniqueID())
+                         },
+                         get_delimiter = function() {
+                           self$header$delimiter
+                         },
+                         validate = function() {
+                           # validate header
+                           private$check_delimiter()
+                           # validate metadata
+                           private$check_metadataHeader()
+                           private$check_key()
+                           private$check_level()
+                           private$check_type()
+                           private$check_label()
+                           # validate data
+                           private$check_dataHeader()
+                           private$check_dataMin()
+                           private$check_dataColumnTypes()
+                         },
+                         initialize = function(header = NULL, metadata, data, validate = TRUE) {
+                           self$header <- header
+                           self$metadata <- metadata
+                           self$data <- data
+
+                           # coerce unique_id to character
+                           self$data[, (self$get_uniqueID()) := sapply(.SD, as.character), .SDcols = self$get_uniqueID()]
+
+                           if (validate) self$validate()
+                         }
+                       ),
+                       private = list(
+                         # deep clone to force data.table copy
+                         deep_clone = function(name, value) {
+                           # invoke a deep copy for metadata and data field
+                           if (name %in% c("metadata", "data")) {
+                             data.table::copy(value)
+                           } else {
+                             value
+                           }
+                         },
+                         ## header checks
+                         check_delimiter = function() {
+                           if (is.element("delimiter", names(self$header))) {
+                             # case: no type column/ no type = array
+                             if (!is.element("type", names(self$metadata)) || !is.element("array", self$metadata[["type"]])) {
+                               warning("Found in-field-delimiter '", self$header$delimiter, "' but no type=array columns (in metadata) to apply to.")
+                             }
+                           }
+                         },
+                         ## metadata checks
+                         check_metadataHeader = function() {
+                           # case: invalid column names
+                           valid_names <- c("key", "factor\\d+", "level", "type", "label", "sub_label")
+                           regex <- paste0("^", valid_names, "$", collapse = "|")
+                           invalid_names <- grep(regex, names(self$metadata), invert = TRUE, value = TRUE, perl = TRUE)
+                           if (length(invalid_names) > 0) {
+                             warning("Metadata: Unexpected column names detected: ", paste0(invalid_names, collapse = ", "))
+                           }
+                           # case: missing mandatory column
+                           requires <- c("key", "level")
+                           missing <- !is.element(requires, names(self$metadata))
+                           if (any(missing)) {
+                             stop("Metadata: Mandatory column(s) missing! ", paste0(requires[missing], collapse = ", "))
+                           }
+                         },
+                         check_key = function() {
+                           # case: duplicated keys
+                           if (anyDuplicated(self$metadata[["key"]])) {
+                             stop("Metadata: Duplicate(s) in key detected! The following key(s) are duplicated: ", paste0(unique(self$metadata[["key"]][duplicated(self$metadata[["key"]])]), collapse = ", "))
+                           }
+                           # case: key not in data
+                           missing <- setdiff(self$metadata[["key"]], names(self$data))
+                           if (length(missing) > 0) {
+                             warning("Metadata rows and data columns differ! Following rows are not defined in data: ", paste0(missing, collapse = ", "))
+                           }
+                         },
+                         check_level = function() {
+                           # case: invalid level
+                           valid <- c("feature", "sample", "condition", "contrast")
+                           unknown <- grep(pattern = paste0(valid, collapse = "|"), x = self$metadata[["level"]], perl = TRUE, invert = TRUE, value = TRUE)
+                           if (length(unknown) > 0) {
+                             warning("Metadata: Unknown level(s) found: ", paste0(unknown, collapse = ", "))
+                           }
+                           # case: minimal level requirements (feature + sample|condition|contrast)
+                           if (!is.element("feature", self$metadata[["level"]]) && !any(is.element(c("sample", "condition", "contrast"), self$metadata[["level"]]))) {
+                             stop("Metadata: Minimum level requirements not met! At least one feature (unique_id) and one sample, condition or contrast needed.")
+                           }
+                         },
+                         check_type = function() {
+                           if (is.element("type", names(self$metadata))) {
+                             feature_types <- c("unique_id", "name", "category", "array")
+                             remaining_types <- c("score", "ratio", "probability", "array")
+                             # case: type doesn't fit level
+                             # select and return keys with unknown type
+                             unknown <- self$metadata[level == "feature"][!type %in% feature_types][["key"]]
+                             unknown <- append(unknown, self$metadata[level %in% c("sample", "condition", "contrast")][!type %in% remaining_types][["key"]])
+                             if (length(unknown) > 0) {
+                               warning("Metadata: Level doesn't match type:", paste0(unknown, collapse = ", "))
+                             }
+                             # case: no unique_id defined
+                             if (!is.element("unique_id", self$metadata[["type"]])) {
+                               stop("Metadata: No unique_id defined in type! Please define a unique_id.")
+                             }
+                             # case: type = array but no delimiter
+                             if (is.element("array", self$metadata[["type"]]) && !is.element("delimiter", names(self$header))) {
+                               stop("Found type=array but no delimiter! Columns with multi-value fields require delimiter (in header) and type=array (in metadata).")
+                             }
+                           }
+                         },
+                         check_label = function() {
+                           if (is.element("label", names(self$metadata))) {
+                             # case: contrast label not delimited by '|'
+                             contrast_labels <- grep(pattern = "\\|", x = self$metadata[level == "contrast"][["label"]], perl = TRUE, invert = TRUE, value = TRUE)
+                             if (length(contrast_labels) > 0) {
+                               warning("Metadata: Missing '|' delimiter in contrast label(s): ", paste0(contrast_labels, collapse = ", "))
+                             }
+                           }
+                         },
+                         ## data checks
+                         check_dataHeader = function() {
+                           # case: column not defined in metadata
+                           missing <- setdiff(names(self$data), self$metadata[["key"]])
+                           if (length(missing) > 0) {
+                             warning("Metadata rows and data columns differ! Following rows are missing in metadata: ", paste0(missing, collapse = ", "))
+                           }
+                           # case: duplicated column names
+                           if (anyDuplicated(names(self$data))) {
+                             stop("Data: Column names not unique! Following names occur more than once: ", paste0(unique(names(self$data)[duplicated(names(self$data))]), collapse = ", "))
+                           }
+                         },
+                         check_dataMin = function() {
+                           # case: minimum requirements not met (two columns: feature(unique_id) + sample|condition|contrast)
+                           if (ncol(self$data) < 2) {
+                             stop("Data: Minimum requirements not met! At least two columns needed, one with unique identifier and one with numeric values.")
+                           }
+                         },
+                         check_dataColumnTypes = function() {
+                           # case: level = sample, condition, contrast not numeric
+                           # except type=array because of delimiter
+                           if (is.element("type", names(self$metadata))) {
+                             expected_numeric_cols <- self$metadata[level %in% c("sample", "condition", "contrast")][type != "array"][["key"]]
+                           } else {
+                             expected_numeric_cols <- self$metadata[level %in% c("sample", "condition", "contrast")][["key"]]
+                           }
+                           not_numeric <- names(self$data[, expected_numeric_cols, with = FALSE][, which(!sapply(self$data[, expected_numeric_cols, with = FALSE], is.numeric))])
+                           if (length(not_numeric) > 0) {
+                             stop("Data: Column(s): ", paste0(not_numeric, collapse = ", "), " not numeric! Probably wrong decimal separator.")
+                           }
+                         }
+                       ),
+                       lock_class = TRUE # prevent class modification
+)
diff --git a/man/Clarion.Rd b/man/Clarion.Rd
new file mode 100644
index 0000000..f02070a
--- /dev/null
+++ b/man/Clarion.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clarion.R
+\docType{data}
+\name{Clarion}
+\alias{Clarion}
+\title{Clarion R6-class definition}
+\format{An object of class \code{R6ClassGenerator} of length 24.}
+\usage{
+Clarion
+}
+\arguments{
+\item{header}{A named list. Defaults to NULL.}
+
+\item{metadata}{Clarion metadata in form of a data.table.}
+
+\item{data}{Data.table according to metadata.}
+
+\item{validate}{Logical value to validate on initialization. Defaults to TRUE.}
+}
+\description{
+Use this to create a clarion object.
+This object is used by all top-level wilson modules.
+}
+\examples{
+# initializing a new object
+object <- Clarion$new(header, metadata, data, validate = TRUE)
+
+# create a deep copy
+object_copy <- object$clone(deep = TRUE)
+
+}
+\keyword{datasets}

From 693dcd499640ce0626f7e0bfbe24849023549247 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Mon, 7 May 2018 09:18:32 +0200
Subject: [PATCH 03/75] parser: return clarion object

---
 R/parser.R | 108 +++++++----------------------------------------------
 1 file changed, 14 insertions(+), 94 deletions(-)

diff --git a/R/parser.R b/R/parser.R
index dbde275..9136f9f 100644
--- a/R/parser.R
+++ b/R/parser.R
@@ -294,7 +294,7 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
 #' @param file Path to file that needs parsing.
 #' @param dec The decimal separator. See \code{\link[data.table]{fread}}.
 #'
-#' @return named list containing list(header = list(), metadata = data.table, data = data.table)
+#' @return Clarion object. See \code{\link[wilson]{Clarion}}
 #'
 #' @import data.table
 #'
@@ -302,18 +302,18 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
 parser <- function(file, dec = ".") {
   message(paste("Parsing file:", file))
 
-  #number of rows for each part
+  # number of rows for each part
   con <- file(file, open = "r")
   num.header <- 0
   num.metadata <- 0
 
   tryCatch(expr = {
-    while(TRUE) {
+    while (TRUE) {
       line <- readLines(con = con, n = 1)
 
-      if(grepl("^!", line, perl = TRUE)) {
+      if (grepl("^!", line, perl = TRUE)) {
         num.header <- num.header + 1
-      } else if(grepl("^#", line, perl = TRUE)) {
+      } else if (grepl("^#", line, perl = TRUE)) {
         num.metadata <- num.metadata + 1
       } else {
         break
@@ -323,11 +323,11 @@ parser <- function(file, dec = ".") {
     close(con = con)
   })
 
-  ###parse header
+  ### parse header
   header <- data.table::fread(input = file, fill = TRUE, header = FALSE, dec = dec, nrows = num.header, integer64 = "double")
-  #cut of leading !
+  # cut of leading !
   header <- as.list(gsub("^!", "", header[[1]]))
-  #make named list
+  # make named list
   header.names <- gsub("=.*$", "", header, perl = TRUE)
   header <- as.list(gsub("^.*?=", "", header, perl = TRUE))
   names(header) <- header.names
@@ -336,104 +336,24 @@ parser <- function(file, dec = ".") {
     header$delimiter <- substr(header$delimiter, start = 2, stop = nchar(header$delimiter) - 1)
   }
 
-  ###parse metadata
+  ### parse metadata
   metadata <- data.table::fread(input = file, skip = num.header, header = FALSE, nrows = num.metadata, fill = TRUE, dec = dec, integer64 = "double")
-  #cut off leading #
+  # cut off leading #
   metadata[, names(metadata)[1] := gsub("^#", "", metadata[[1]])]
-  #set first line as header
+  # set first line as header
   names(metadata) <- as.character(metadata[1])
 
   # remove empty columns
   metadata <- metadata[, which(unlist(lapply(metadata, function(x) !all(is.na(x) || x == "")))), with = FALSE]
 
-  #check for unexpected columns
-  accepted_columns <- c("key", "factor\\d+", "level", "type", "label", "sub_label")
-  regex <- paste0(paste0("^", accepted_columns, "$"), collapse = "|")
-  invalid <- grep(regex, names(metadata), invert = TRUE, perl = TRUE)
-  if(length(invalid) > 0){
-    warning(paste("Metadata: Unexpected columnames detected: ", paste0(names(metadata)[invalid], collapse = ", ")))
-  }
-  # check mandatory columns
-  check_columns <- c("key", "level")
-  mandatory <- check_columns %in% names(metadata)
-  if(!all(mandatory)) {
-    stop(paste0("Metadata: Mandatory column(s) are missing! ", paste0(check_columns[!mandatory], collapse = ", ")))
-  }
-
-  #delete first line
+  # delete first line
   metadata <- metadata[-1]
-  # duplicated keys?
-  meta_duplicants <- duplicated(metadata[["key"]])
-  if(any(meta_duplicants)) {
-    stop(paste0("Metadata: Duplicate(s) in key detected! The following keys occur more than once: ", paste0(unique(metadata[["key"]][meta_duplicants]), collapse = ", ")))
-  }
-
-  # check levels
-  known_level <- c("feature", "sample", "condition", "contrast")
-  unknown_level <- metadata[!level %in% known_level][["level"]]
-  if(length(unknown_level) > 0) {
-    warning(paste0("Metadata: Unkown level found: ", paste0(unknown_level, collapse = ", ")))
-  }
-  # check if type fits corresponding level
-  if(is.element("type", names(metadata))) {
-    # if type contains array delimiter mandatory
-    if(is.element("array", metadata[["type"]])) {
-      if(!is.element("delimiter", names(header))) {
-        stop("Found array but no delimiter! Multi-value fields require delimiter (in header) and type (in metadata).")
-      }
-    }
-    # feature
-    feature_types <- c("unique_id", "name", "category", "array")
-    # sample, condition, contrast
-    samp_cond_cont_types <- c("score", "ratio", "probability", "array")
-
-    keys <- metadata[level == "feature" & !type %in% feature_types][["key"]]
-    keys <- append(keys, metadata[level %in% c("sample", "condition", "contrast") & !type %in% samp_cond_cont_types][["key"]])
-
-    # unique_id defined?
-    if(!is.element("unique_id", metadata[["type"]])) {
-      stop("Metadata: No unique_id found in type! Please define an unique_id.")
-    }
-
-    if(length(keys) > 0) {
-      warning(paste0("Metadata: Level doesn't match type: ", paste0(keys, collapse = ", ")))
-    }
-  }
-
-  ###parse data
-  # check for inconsistency
-  col_data <- data.table::fread(input = file, header = TRUE, skip = num.header + num.metadata, fill = FALSE, nrows = 0, dec = dec, integer64 = "double")
-  col_names <- names(col_data)
-  missing_refs <- setdiff(col_names, metadata[[1]])
-  missing_cols <- setdiff(metadata[[1]], col_names)
-  if(length(missing_refs) > 0) {
-    warning(paste0("Metadata rows and data columns differ! Following rows are missing in metadata: ", paste(missing_refs, collapse = ", ")))
-  }
-  if(length(missing_cols) > 0) {
-    warning(paste0("Metadata rows and data columns differ! Following columns are not definded in data: ", paste(missing_refs, collapse = ", ")))
-  }
-  # duplicated columnnames?
-  data_duplicants <- duplicated(col_names)
-  if(any(data_duplicants)) {
-    stop(paste0("Data: Duplicated column name(s) detected! The following names are duplicated: ", paste0(unique(col_names[data_duplicants]), collapse = ", ")))
-  }
 
+  ### parse data
   data <- data.table::fread(input = file, header = TRUE, skip = num.header + num.metadata, fill = FALSE, dec = dec, integer64 = "double")
 
-  # unexpected columntypes?; sample, condition & contrast numeric?
-  if(is.element("type", names(metadata))) {
-    columns <- metadata[level %in% c("sample", "condition", "contrast") & type != "array"][["key"]]
-  } else {
-    columns <- metadata[level %in% c("sample", "condition", "contrast")][["key"]]
-  }
-  not_num_cols <- names(data[, columns, with = FALSE][, which(!sapply(data[, columns, with = FALSE], is.numeric))])
-  if(length(not_num_cols) > 0) {
-    stop(paste0("Column(s): ", paste0(not_num_cols, collapse = ", "), " not numeric! Probably wrong decimal separator."))
-  }
-
   data.table::setindexv(metadata, names(metadata)[1])
   data.table::setindexv(data, names(data)[1])
 
-  return(list(header = header, metadata = metadata, data = data))
+  return(Clarion$new(header = header, metadata = metadata, data = data))
 }
-

From 41586525ba1834fea68d4efd1c36010ad642a478 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Mon, 7 May 2018 09:24:11 +0200
Subject: [PATCH 04/75] parser: no header = NULL (not empty named list)

---
 R/parser.R | 24 ++++++++++++++----------
 1 file changed, 14 insertions(+), 10 deletions(-)

diff --git a/R/parser.R b/R/parser.R
index 9136f9f..da86729 100644
--- a/R/parser.R
+++ b/R/parser.R
@@ -324,16 +324,20 @@ parser <- function(file, dec = ".") {
   })
 
   ### parse header
-  header <- data.table::fread(input = file, fill = TRUE, header = FALSE, dec = dec, nrows = num.header, integer64 = "double")
-  # cut of leading !
-  header <- as.list(gsub("^!", "", header[[1]]))
-  # make named list
-  header.names <- gsub("=.*$", "", header, perl = TRUE)
-  header <- as.list(gsub("^.*?=", "", header, perl = TRUE))
-  names(header) <- header.names
-  # remove quotes from delimiter
-  if (!is.null(header$delimiter) && grepl(header$delimiter, pattern = '^".*"$', perl = TRUE)) {
-    header$delimiter <- substr(header$delimiter, start = 2, stop = nchar(header$delimiter) - 1)
+  if (num.header > 0) {
+    header <- data.table::fread(input = file, fill = TRUE, header = FALSE, dec = dec, nrows = num.header, integer64 = "double")
+    # cut of leading !
+    header <- as.list(gsub("^!", "", header[[1]]))
+    # make named list
+    header.names <- gsub("=.*$", "", header, perl = TRUE)
+    header <- as.list(gsub("^.*?=", "", header, perl = TRUE))
+    names(header) <- header.names
+    # remove quotes from delimiter
+    if (!is.null(header$delimiter) && grepl(header$delimiter, pattern = '^".*"$', perl = TRUE)) {
+      header$delimiter <- substr(header$delimiter, start = 2, stop = nchar(header$delimiter) - 1)
+    }
+  } else {
+    header <- NULL
   }
 
   ### parse metadata

From beb67a2256fc24b73f3a93b7195dcc349ad16047 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Mon, 7 May 2018 11:47:49 +0200
Subject: [PATCH 05/75] clarion: added is_delimited function

---
 R/clarion.R | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/R/clarion.R b/R/clarion.R
index cedc7a9..39f1d6e 100644
--- a/R/clarion.R
+++ b/R/clarion.R
@@ -41,6 +41,13 @@ Clarion <- R6::R6Class("Clarion",
                          get_delimiter = function() {
                            self$header$delimiter
                          },
+                         is_delimited = function(x) {
+                           if (is.element("type", names(self$metadata))) {
+                             return(self$metadata[key == x] == "array")
+                           } else {
+                             return(FALSE)
+                           }
+                         },
                          validate = function() {
                            # validate header
                            private$check_delimiter()

From 8849cd7888d62dc6c1426c1193ea0f32823a4d7c Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Mon, 7 May 2018 12:30:25 +0200
Subject: [PATCH 06/75] parser: updated  documentation

---
 man/parser.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/parser.Rd b/man/parser.Rd
index 4700c2b..6c17acb 100644
--- a/man/parser.Rd
+++ b/man/parser.Rd
@@ -12,7 +12,7 @@ parser(file, dec = ".")
 \item{dec}{The decimal separator. See \code{\link[data.table]{fread}}.}
 }
 \value{
-named list containing list(header = list(), metadata = data.table, data = data.table)
+Clarion object. See \code{\link[wilson]{Clarion}}
 }
 \description{
 Method to parse input file.

From 70bfa601516cf8a706b4935d670f3092f0634f4c Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Mon, 7 May 2018 12:30:50 +0200
Subject: [PATCH 07/75] featureSelector: use clarion object

---
 R/featureSelector.R            | 122 ++++++++++++++-------------------
 exec/featureSelector_example.R |  13 +++-
 man/featureSelector.Rd         |  15 ++--
 man/featureSelectorGuide.Rd    |   2 -
 4 files changed, 66 insertions(+), 86 deletions(-)

diff --git a/R/featureSelector.R b/R/featureSelector.R
index 13fea96..74b9107 100644
--- a/R/featureSelector.R
+++ b/R/featureSelector.R
@@ -48,64 +48,53 @@ featureSelectorUI <- function(id){
 #' @param input Shiny's input object.
 #' @param output Shiny's output object.
 #' @param session Shiny's session object.
-#' @param data data.table from which to select (Supports reactive).
-#' @param features List of features (i.e. columnnames) the and module will show (Defaults to names(data))(Supports reactive).
-#' @param feature.grouping Display features seperated in boxes. (Data.table: first column = columnnames, second column = groupnames) (Supports reactive)
-#' @param delimiter A single character, or a vector indicating how column values are delimited. (Fills vector sequentially if needed)(Supports reactive)
+#' @param clarion A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)
 #' @param multiple Whether or not textual ORs should allow multiple selections. (Fills vector sequentially if needed)(Supports reactive)
 #' @param contains Whether or not textual ORs are initialized as textInput checking entries for given string. (Fills vector sequentially if needed)(Supports reactive)
 #' @param ranged Whether or not numeric ORs are ranged. (Fills vector sequentially if needed)(Supports reactive)
-#' @param step Set numeric ORs slider steps. (Fills vector sequentially if needed)(Supports reactive)
+#' @param step Set numeric ORs number of slider steps. (Fills vector sequentially if needed)(Supports reactive)
 #' @param truncate Truncate datatable entries at x characters (Default = 30).
 #' @param selection.default Decide whether everything or nothing is selected on default (no filters applied). Either "all" or "none" (Default = "all").
 #'
 #' @details Keep in mind that the order of features is the order in which delimiter, multiple, contains, ranged and step are evaluated.
 #'
-#' @return Reactive containing names list: Selected data as reactive containing data.table (data). Used filter to select data (filter).
+#' @return Reactive containing names list: Selected data as reactive containing clarion object (object). Used filter to select data (filter).
 #'
 #' @export
-featureSelector <- function(input, output, session, data, features = NULL, feature.grouping = NULL, delimiter = "|", multiple = TRUE, contains = FALSE, ranged = TRUE, step = 100, truncate = 30, selection.default = "all"){
-  # handle reactive data
-  data.r <- shiny::reactive({
-    if(shiny::is.reactive(data)){
-      data.table::copy(data())
-    }else{
-      data.table::copy(data)
+featureSelector <- function(input, output, session, clarion, multiple = TRUE, contains = FALSE, ranged = TRUE, step = 100, truncate = 30, selection.default = "all"){
+  # object/ data preparation
+  object <- shiny::reactive({
+    # support reactive
+    if (shiny::is.reactive(clarion)) {
+      if (!methods::is(clarion(), "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
+
+      obj <- clarion()$clone(deep = TRUE)
+    } else {
+      if (!methods::is(clarion, "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
+
+      obj <- clarion$clone(deep = TRUE)
     }
   })
 
-  # handle reactive features
-  features.r <- shiny::reactive({
-    if(is.null(features)){
-      names(data.r())
-    }else{
-      if(shiny::is.reactive(features)){
-        if(is.null(features())){
-          names(data.r())
-        }else{
-          features()
-        }
-      }else{
-        features
+  # delimiter vector
+  # only delimit type = array
+  delimiter <- shiny::reactive({
+    sapply(names(object()$data), function(x) {
+      if (object()$is_delimited(x)) {
+        return(object()$get_delimiter())
+      } else {
+        return(NULL)
       }
-    }
+    })
   })
 
-  # handle reactive grouping
-  feature.grouping.r <- shiny::reactive({
-    if(shiny::is.reactive(feature.grouping)){
-      feature.grouping()
-    }else{
-      feature.grouping
-    }
-  })
 
-  and_selected <- shiny::callModule(and, "and", data = data.r, show.elements = features.r, element.grouping = feature.grouping.r, delimiter = delimiter, multiple = multiple, contains = contains, ranged = ranged, step = step, reset = shiny::reactive(input$reset))
+  and_selected <- shiny::callModule(and, "and", data = shiny::reactive(object()$data), element.grouping = shiny::reactive(object()$metadata[, c("key", "level")]), delimiter = delimiter, multiple = multiple, contains = contains, ranged = ranged, step = step, reset = shiny::reactive(input$reset))
   row_selector <- shiny::callModule(orNumeric, "row_selector", choices = choices, value = value_wrapper, label = "Select n features from the top and/or bottom of the list", stepsize = 1)
 
   # row_selector choices
   choices <- shiny::reactive({
-    if(nrow(data_output()$data) > 0) {
+    if (nrow(data_output()$data) > 0) {
       c(1:nrow(data_output()$data))
     } else {
       c(0, 0)
@@ -117,7 +106,7 @@ featureSelector <- function(input, output, session, data, features = NULL, featu
 
   # select all if no values stored
   value_wrapper <- shiny::reactive({
-    if(is.null(value())) {
+    if (is.null(value())) {
       value(c(min(choices()), max(choices())))
     }
 
@@ -126,8 +115,8 @@ featureSelector <- function(input, output, session, data, features = NULL, featu
 
   # safe row_selector value
   shiny::observeEvent(input$select, {
-    if(shiny::isTruthy(input$table_rows_selected)) {
-      if(grepl("outer", row_selector()$text)) { # accomodate for outer selection
+    if (shiny::isTruthy(input$table_rows_selected)) {
+      if (grepl("outer", row_selector()$text)) { # accomodate for outer selection
         diff <- setdiff(input$table_rows_all, input$table_rows_selected)
         value(c(min(diff), max(diff)))
       } else {
@@ -138,7 +127,7 @@ featureSelector <- function(input, output, session, data, features = NULL, featu
     }
   })
   # reset row_selector value on data change
-  shiny::observeEvent(data.r(), {
+  shiny::observeEvent(object(), {
     value(NULL)
   })
 
@@ -151,7 +140,7 @@ featureSelector <- function(input, output, session, data, features = NULL, featu
   })
 
   # Fetch reactive guide for this module
-  guide <- featureSelectorGuide(session, !is.null(feature.grouping))
+  guide <- featureSelectorGuide(session)
   shiny::observeEvent(input$guide, {
     rintrojs::introjs(session, options = list(steps = guide(), scrollToElement = FALSE))
   })
@@ -174,7 +163,7 @@ featureSelector <- function(input, output, session, data, features = NULL, featu
           shiny::column(
             width = 1,
             # added css so that padding won't be added everytime (sums up) modal is shown
-            shiny::tags$style(type="text/css", "body {padding-right: 0px !important;}"),
+            shiny::tags$style(type = "text/css", "body {padding-right: 0px !important;}"),
             shiny::actionLink(session$ns("infobutton"), label = NULL, icon = shiny::icon("question-circle"))
           )
         ),
@@ -216,7 +205,7 @@ featureSelector <- function(input, output, session, data, features = NULL, featu
     row_order <- input$table_rows_all
 
     # don't select whole table
-    if(any(row_selector()$bool == FALSE) & length(row_selector()$bool) == length(row_order)) {
+    if (any(row_selector()$bool == FALSE) & length(row_selector()$bool) == length(row_order)) {
       DT::selectRows(proxy, row_order[row_selector()$bool])
     } else {
       # delete selection
@@ -243,15 +232,15 @@ featureSelector <- function(input, output, session, data, features = NULL, featu
   select <- shiny::eventReactive(eventExpr = input$select, {
     log_message(message = "Filtering data", level = "INFO", token = session$token)
 
-    data <- data.r()[and_selected()$bool]
+    data <- object()$data[and_selected()$bool]
   })
 
   # second filter (highlighted rows) selected via click and/ or 'select rows' ui
   result <- shiny::reactive({
     # create subset
-    if(!is.null(input$table_rows_selected)) {
+    if (!is.null(input$table_rows_selected)) {
       data <- data_output()$data[input$table_rows_selected]
-    } else if(!is.null(input$table_rows_all)) {
+    } else if (!is.null(input$table_rows_all)) {
       data <- data_output()$data[input$table_rows_all]
     } else {
       data <- data_output()$data
@@ -261,7 +250,7 @@ featureSelector <- function(input, output, session, data, features = NULL, featu
     filter <- data_output()$filter
 
     # number of rows selected
-    if(!is.null(input$table_rows_selected)) {
+    if (!is.null(input$table_rows_selected)) {
       filter <- append(filter, after = 1,
                        values = paste("Selected:", length(input$table_rows_selected))
                        )
@@ -270,8 +259,8 @@ featureSelector <- function(input, output, session, data, features = NULL, featu
     # TODO add order information to filter
 
     # search text
-    if(!is.null(input$table_search)) {
-      if(nchar(input$table_search) > 0) {
+    if (!is.null(input$table_search)) {
+      if (nchar(input$table_search) > 0) {
         hits <- ifelse(is.null(input$table_rows_all), 0, length(input$table_rows_all))
         filter <- append(filter, after = 1,
                          values = paste("Search:", paste0("'", input$table_search, "'"), paste0("(Hits: ", hits, ")"))
@@ -279,7 +268,7 @@ featureSelector <- function(input, output, session, data, features = NULL, featu
       }
     }
 
-    return(list(data = data, filter = filter))
+    return(list(object = Clarion$new(header = object()$header, metadata = object()$metadata, data = data, validate = FALSE), filter = filter))
   })
 
   # store change
@@ -287,28 +276,28 @@ featureSelector <- function(input, output, session, data, features = NULL, featu
 
   # return on file change unprocessed table
   data_output <- shiny::reactive({
-    if(data_change() == 0) {
-      if(selection.default == "all") {
-        data <- data.r()
-      } else if(selection.default == "none") {
-        data <- data.r()[FALSE]
+    if (data_change() == 0) {
+      if (selection.default == "all") {
+        data <- object()$data
+      } else if (selection.default == "none") {
+        data <- object()$data[FALSE]
       }
 
       # create filter text
       filter <- paste("Result:" , nrow(data), "hits")
-    } else if(data_change() == 1) {
+    } else if (data_change() == 1) {
       data <- select()
 
       # create filter text
       filter <- c(paste("Result:", nrow(data), "hits"), "", shiny::isolate(and_selected()$text))
     }
 
-    return(list(data = data , filter = filter))
+    return(list(data = data, filter = filter))
   })
 
   # observe most recent change
   shiny::observe({
-    data.r()
+    object()$data
     data_change(0)
   })
   shiny::observe({
@@ -322,12 +311,14 @@ featureSelector <- function(input, output, session, data, features = NULL, featu
 #' featureSelector module guide
 #'
 #' @param session The shiny session
-#' @param grouping Logical if Text for grouping should be displayed (Default = FALSE).
 #'
 #' @return A shiny reactive that contains the texts for the guide steps.
 #'
 featureSelectorGuide <- function(session, grouping = FALSE) {
-  steps <- list(
+  steps <- list("guide_and" = "<h4>Grouping</h4>
+      These boxes contain several selectors each.<br/>
+      Expand/ Collapse them with a click on the '+'/ '-' on the right side.<br/>
+      Please expand now one or more of those boxes.",
     "guide_and" = paste0("<h4>Selectors</h4>
       The selectors are presented row-wise, so that each line represents a seperate selector.<br/>
       Each one operates on a single column of the dataset defined by the columnname on the left side.<br/>
@@ -348,14 +339,5 @@ featureSelectorGuide <- function(session, grouping = FALSE) {
       <b>select rows</b>: Either use the slider or directly click on rows to select only certain rows in the table."
   )
 
-  if(grouping) {
-    steps <- append(steps,
-                    list("guide_and" = "<h4>Grouping</h4>
-                          These boxes contain several selectors each.<br/>
-                          Expand/ Collapse them with a click on the '+'/ '-' on the right side.<br/>
-                          Please expand now one or more of those boxes."),
-                    0)
-  }
-
   shiny::reactive(data.frame(element = paste0("#", session$ns(names(steps))), intro = unlist(steps)))
 }
diff --git a/exec/featureSelector_example.R b/exec/featureSelector_example.R
index 1d3cfa6..b60611d 100644
--- a/exec/featureSelector_example.R
+++ b/exec/featureSelector_example.R
@@ -6,16 +6,17 @@ source("../R/orTextual.R")
 source("../R/featureSelector.R")
 source("../R/function.R")
 source("../R/global.R")
+source("../R/clarion.R")
 
 # test data
 data <- data.table::as.data.table(mtcars, keep.rowname = "id")
 # create metadata
-metadata <- data.table::data.table(names(data), type = c("annotation", rep("performance", 7), rep("design", 4)))
+metadata <- data.table::data.table(names(data), level = c("feature", rep("sample", 7), rep("condition", 4)))
 names(metadata)[1] <- "key"
+clarion <- Clarion$new(data = data, metadata = metadata)
 
 ui <- dashboardPage(header = dashboardHeader(),
                     sidebar = dashboardSidebar(
-                      selectInput("columns", label = "Features to select from", choices = names(data), multiple = TRUE),
                       verbatimTextOutput("filter")
 ), dashboardBody(fluidPage(
   featureSelectorUI(id = "id")
@@ -24,12 +25,18 @@ ui <- dashboardPage(header = dashboardHeader(),
 
 server <- function(input, output) {
 
-  mod <-callModule(featureSelector, "id", data = data, delimiter = ",", features = reactive(input$columns), feature.grouping = metadata)
+  mod <- callModule(featureSelector, "id", clarion = clarion)
 
   output$filter <- renderText({
     paste(mod()$filter, collapse = "\n")
   })
 
+  observe({
+    print(mod()$object$header)
+    print(mod()$object$metadata)
+    print(mod()$object$data)
+  })
+
 }
 
 # Run the application
diff --git a/man/featureSelector.Rd b/man/featureSelector.Rd
index c52d853..3a53695 100644
--- a/man/featureSelector.Rd
+++ b/man/featureSelector.Rd
@@ -4,8 +4,7 @@
 \alias{featureSelector}
 \title{featureSelector module server logic}
 \usage{
-featureSelector(input, output, session, data, features = NULL,
-  feature.grouping = NULL, delimiter = "|", multiple = TRUE,
+featureSelector(input, output, session, clarion, multiple = TRUE,
   contains = FALSE, ranged = TRUE, step = 100, truncate = 30,
   selection.default = "all")
 }
@@ -16,13 +15,7 @@ featureSelector(input, output, session, data, features = NULL,
 
 \item{session}{Shiny's session object.}
 
-\item{data}{data.table from which to select (Supports reactive).}
-
-\item{features}{List of features (i.e. columnnames) the and module will show (Defaults to names(data))(Supports reactive).}
-
-\item{feature.grouping}{Display features seperated in boxes. (Data.table: first column = columnnames, second column = groupnames) (Supports reactive)}
-
-\item{delimiter}{A single character, or a vector indicating how column values are delimited. (Fills vector sequentially if needed)(Supports reactive)}
+\item{clarion}{A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)}
 
 \item{multiple}{Whether or not textual ORs should allow multiple selections. (Fills vector sequentially if needed)(Supports reactive)}
 
@@ -30,14 +23,14 @@ featureSelector(input, output, session, data, features = NULL,
 
 \item{ranged}{Whether or not numeric ORs are ranged. (Fills vector sequentially if needed)(Supports reactive)}
 
-\item{step}{Set numeric ORs slider steps. (Fills vector sequentially if needed)(Supports reactive)}
+\item{step}{Set numeric ORs number of slider steps. (Fills vector sequentially if needed)(Supports reactive)}
 
 \item{truncate}{Truncate datatable entries at x characters (Default = 30).}
 
 \item{selection.default}{Decide whether everything or nothing is selected on default (no filters applied). Either "all" or "none" (Default = "all").}
 }
 \value{
-Reactive containing names list: Selected data as reactive containing data.table (data). Used filter to select data (filter).
+Reactive containing names list: Selected data as reactive containing clarion object (object). Used filter to select data (filter).
 }
 \description{
 featureSelector module server logic
diff --git a/man/featureSelectorGuide.Rd b/man/featureSelectorGuide.Rd
index 1bdba64..77e27be 100644
--- a/man/featureSelectorGuide.Rd
+++ b/man/featureSelectorGuide.Rd
@@ -8,8 +8,6 @@ featureSelectorGuide(session, grouping = FALSE)
 }
 \arguments{
 \item{session}{The shiny session}
-
-\item{grouping}{Logical if Text for grouping should be displayed (Default = FALSE).}
 }
 \value{
 A shiny reactive that contains the texts for the guide steps.

From 9d164fb1b6c80e5636bfa7e591d48f6fd0b4a63c Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Tue, 8 May 2018 11:58:47 +0200
Subject: [PATCH 08/75] clarion: get_factors function added

---
 R/clarion.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/clarion.R b/R/clarion.R
index 39f1d6e..05989a7 100644
--- a/R/clarion.R
+++ b/R/clarion.R
@@ -48,6 +48,9 @@ Clarion <- R6::R6Class("Clarion",
                              return(FALSE)
                            }
                          },
+                         get_factors = function() {
+                           grep("^factor\\d+", names(self$metadata), perl = TRUE, value = TRUE)
+                         },
                          validate = function() {
                            # validate header
                            private$check_delimiter()

From d54d9ad9929aaa2c721a0e1b9d9562b9c9ab0038 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Tue, 8 May 2018 12:04:52 +0200
Subject: [PATCH 09/75] geneView: integrated clarion object; choose grouping
 factor

---
 R/geneView.R            | 328 ++++++++++++++++++----------------------
 exec/geneView_example.R |  20 +--
 man/geneView.Rd         |  20 +--
 man/geneViewGuide.Rd    |   4 +-
 4 files changed, 160 insertions(+), 212 deletions(-)

diff --git a/R/geneView.R b/R/geneView.R
index 55f64c0..5d9964a 100644
--- a/R/geneView.R
+++ b/R/geneView.R
@@ -39,6 +39,7 @@ geneViewUI <- function(id, plot.columns = 3){
               width = 3,
               shiny::div(id = ns("guide_columnSelection"),
                          columnSelectorUI(ns("selector"), title = "Grouping:"),
+                         labelUI(ns("group")),
                          shiny::selectInput(ns("groupby"), label = "by", choices = c("gene", "condition"))
               )
             ),
@@ -83,17 +84,8 @@ geneViewUI <- function(id, plot.columns = 3){
 #' @param input Shiny's input object.
 #' @param output Shiny's output object.
 #' @param session Shiny's session object.
-#' @param data data.table:
-#'                        column1   : ids
-#'                        column2   : symbol (data used for selection)
-#'                        column3-n : data
-#' @param metadata data.table:
-#'                            column1: ids
-#'                            column2: factor1 (conditions)
-#'                            column3: level (condition type)
-#' @param level Vector containing data levels to select from (default: unique(metadata[["level"]])).
+#' @param clarion A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)
 #' @param plot.method Choose which method is used for plotting. Either "static" or "interactive" (Default = "static").
-#' @param custom.label Data.table used for creating custom labels (supports reactive).
 #' @param label.sep Seperator used for label merging (Default = ", ").
 #' @param width Width of the plot in cm. Defaults to minimal size for readable labels and supports reactive.
 #' @param height Height of the plot in cm. Defaults to minimal size for readable labels and supports reactive.
@@ -106,32 +98,26 @@ geneViewUI <- function(id, plot.columns = 3){
 #' @return Reactive containing data.table used for plotting.
 #'
 #' @export
+geneView <- function(input, output, session, clarion, plot.method = "static", label.sep = ", ", width = "auto", height = "auto", ppi = 72, scale = 1){
+  # globals/ initialization #####
+  clearPlot <- shiny::reactiveVal(FALSE)
+  # disable downloadButton on init
+  shinyjs::disable("download")
 
-geneView <- function(input, output, session, data, metadata, level = NULL, plot.method = "static", custom.label = NULL, label.sep = ", ", width = "auto", height = "auto", ppi = 72, scale = 1){
-  #handle reactive data
-  data.r <- shiny::reactive({
-    if(shiny::is.reactive(data)){
-      data.table::copy(data())
-    }else{
-      data.table::copy(data)
-    }
-  })
-  metadata.r <- shiny::reactive({
-    if(shiny::is.reactive(metadata)){
-      metadata()
-    }else{
-      metadata
-    }
-  })
-  level.r <- shiny::reactive({
-    if(is.null(level)){
-      metadata[[3]]
-    }else if(shiny::is.reactive(level)){
-      level()
-    }else{
-      level
+  # input preparation #####
+  object <- shiny::reactive({
+    # support reactive
+    if (shiny::is.reactive(clarion)) {
+      if (!methods::is(clarion(), "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
+
+      obj <- clarion()$clone(deep = TRUE)
+    } else {
+      if (!methods::is(clarion, "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
+
+      obj <- clarion$clone(deep = TRUE)
     }
   })
+
   # handle reactive sizes
   size <- shiny::reactive({
     width <- ifelse(shiny::is.reactive(width), width(), width)
@@ -139,13 +125,13 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
     ppi <- ifelse(shiny::is.reactive(ppi), ppi(), ppi)
     scale <- ifelse(shiny::is.reactive(scale), scale(), scale)
 
-    if(!is.numeric(width) || width <= 0) {
+    if (!is.numeric(width) || width <= 0) {
       width <- "auto"
     }
-    if(!is.numeric(height) || height <= 0) {
+    if (!is.numeric(height) || height <= 0) {
       height <- "auto"
     }
-    if(!is.numeric(ppi) || ppi <= 0) {
+    if (!is.numeric(ppi) || ppi <= 0) {
       ppi <- 72
     }
 
@@ -155,49 +141,18 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
          scale = scale)
   })
 
-  #Fetch the reactive guide for this module
-  guide <- geneViewGuide(session, label = !is.null(custom.label))
-  shiny::observeEvent(input$guide, {
-    rintrojs::introjs(session, options = list(steps = guide()))
-  })
-
-  # clear plot
-  clearPlot <- shiny::reactiveVal(FALSE)
-
-  # reset
-  shiny::observeEvent(input$reset, {
-    log_message("GeneView: reset", "INFO", token = session$token)
-
-    shinyjs::reset("genes")
-    shinyjs::reset("plotType")
-    shinyjs::reset("groupby")
-    shinyjs::reset("plotColumns")
-    colorPicker <<- shiny::callModule(colorPicker2, "color", distribution = "all", selected = "Dark2")
-    transform <<- shiny::callModule(transformation, "transform", shiny::reactive(as.matrix(data.r()[, selector$selectedColumns(), with = FALSE])))
-    selector <<- shiny::callModule(columnSelector, "selector", type.columns = shiny::reactive(metadata.r()[level %in% level.r(), c(1, 3)]), columnTypeLabel = "Select Columns")
-    if(!is.null(custom.label)) {
-      custom_label <<- shiny::callModule(label, "labeller", data = custom.label, sep = label.sep)
-    }
-    limiter <<- shiny::callModule(limit, "limit", lower = shiny::reactive(get_limits()[1]), upper = shiny::reactive(get_limits()[2]))
-    clearPlot(TRUE)
-  })
-
-  get_limits <- shiny::reactive({
-    equalize(result.data()$data[, c(-1, -2)])
-  })
-
+  # modules/ ui #####
   colorPicker <- shiny::callModule(colorPicker2, "color", distribution = "all", selected = "Dark2")
-  transform <- shiny::callModule(transformation, "transform", shiny::reactive(as.matrix(data.r()[, selector$selectedColumns(), with = FALSE])))
-  selector <- shiny::callModule(columnSelector, "selector", type.columns = shiny::reactive(metadata.r()[level %in% level.r(), c(1, 3)]), columnTypeLabel = "Select Columns")
-  if(!is.null(custom.label)) {
-    custom_label <- shiny::callModule(label, "labeller", data = custom.label, sep = label.sep)
-  }
+  transform <- shiny::callModule(transformation, "transform", shiny::reactive(as.matrix(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes), selector$selectedColumns(), with = FALSE])))
+  selector <- shiny::callModule(columnSelector, "selector", type.columns = shiny::reactive(object()$metadata[level != "feature", c("key", "level")]), columnTypeLabel = "Select Columns")
+  custom_label <- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes)]), sep = label.sep)
+  factor_data <- shiny::callModule(label, "group", label = "Select grouping factors", data = shiny::reactive(object()$metadata[key %in% selector$selectedColumns(), c(object()$get_factors())]), sep = label.sep, unique = FALSE)
   limiter <- shiny::callModule(limit, "limit", lower = shiny::reactive(get_limits()[1]), upper = shiny::reactive(get_limits()[2]))
 
   output$genes <- shiny::renderUI({
     output <- shiny::selectizeInput(session$ns("genes"), label = "Select Genes", choices = NULL, multiple = TRUE)
-    #only fetch needed data (calculation on server-side)
-    shiny::updateSelectizeInput(session, "genes", choices = unique(data.r()[[2]]), server = TRUE)
+    # only fetch needed data (calculation on server-side)
+    shiny::updateSelectizeInput(session, "genes", choices = unique(object()$data[[object()$get_name()]]), server = TRUE)
 
     # colored if not has item
     output <- shiny::div(class = "empty", output)
@@ -205,63 +160,52 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
     return(output)
   })
 
-  output$level <- shiny::renderUI({
-    shiny::selectInput(session$ns("level"), label = "Data level", choices = unique(level.r()))
-  })
-
   shiny::observe({
     shiny::updateTextInput(session = session, inputId = "label", value = transform$method())
   })
 
-  #notification
-  shiny::observe({
-    shiny::req(input$genes)
-
-    if(length(input$genes) > 50){
-      shiny::showNotification(
-        paste("Caution! You selected", length(input$genes), "genes. This may take a while to compute."),
-        duration = 5,
-        type = "warning",
-        id = "warning",
-        closeButton = FALSE
-      )
-    }else{
-      shiny::removeNotification("warning")
+  output$geneView <- shiny::renderUI({
+    if (plot.method == "interactive") {
+      shinycssloaders::withSpinner(plotly::plotlyOutput(session$ns("interactive")), proxy.height = "800px")
+    } else if (plot.method == "static") {
+      shinycssloaders::withSpinner(shiny::plotOutput(session$ns("static")), proxy.height = "800px")
     }
   })
 
-  # warning if plot size exceeds limits
-  shiny::observe({
-    if(plot()$exceed_size) {
-      shiny::showNotification(
-        ui = "Width and/ or height exceed limit. Using 500 cm instead.",
-        id = "limit",
-        type = "warning"
-      )
-    } else {
-      shiny::removeNotification("limit")
-    }
+  # functionality/ plotting #####
+  # reset
+  shiny::observeEvent(input$reset, {
+    log_message("GeneView: reset", "INFO", token = session$token)
+
+    shinyjs::reset("genes")
+    shinyjs::reset("plotType")
+    shinyjs::reset("groupby")
+    shinyjs::reset("plotColumns")
+    colorPicker <<- shiny::callModule(colorPicker2, "color", distribution = "all", selected = "Dark2")
+    transform <<- shiny::callModule(transformation, "transform", shiny::reactive(as.matrix(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes), selector$selectedColumns(), with = FALSE])))
+    selector <<- shiny::callModule(columnSelector, "selector", type.columns = shiny::reactive(object()$metadata[level != "feature", c("key", "level")]), columnTypeLabel = "Select Columns")
+    custom_label <<- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes)]), sep = label.sep)
+    factor_data <<- shiny::callModule(label, "group", label = "Select grouping factors", data = shiny::reactive(object()$metadata[key %in% selector$selectedColumns(), c(object()$get_factors())]), sep = label.sep, unique = FALSE)
+    limiter <<- shiny::callModule(limit, "limit", lower = shiny::reactive(get_limits()[1]), upper = shiny::reactive(get_limits()[2]))
+    clearPlot(TRUE)
+  })
+
+  get_limits <- shiny::reactive({
+    equalize(result.data()$data[, c(-1, -2)])
   })
 
   result.data <- shiny::eventReactive(input$plot, {
-    result <- data.table::data.table(data.r()[, c(1, 2)], data.table::as.data.table(transform$data()))
+    columns <- switch((object()$get_uniqueID() == object()$get_name()) + 1,
+                      c(object()$get_uniqueID(), object()$get_name()),
+                      object()$get_uniqueID())
 
-    # label selected?
-    if(!is.null(custom.label)) {
-      # drop not selected
-      label <- custom_label()$label[which(result[[2]] %in% input$genes)]
-    } else {
-      label <- NULL
-    }
+    result <- data.table::data.table(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes), columns, with = FALSE], data.table::as.data.table(transform$data()))
 
-    result <- result[result[[2]] %in% input$genes]
+    label <- custom_label()$label
 
     return(list(data = result, label = label))
   })
 
-  # disable downloadButton on init
-  shinyjs::disable("download")
-
   plot <- shiny::eventReactive(input$plot, {
     log_message("GeneView: computing plot...", "INFO", token = session$token)
 
@@ -269,22 +213,25 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
     shinyjs::enable("download")
     clearPlot(FALSE)
 
-    #new progress indicator
+    # new progress indicator
     progress <- shiny::Progress$new()
     on.exit(progress$close())
     progress$set(0, message = "Computing data")
 
-    processed.data <- data.table::copy(result.data()$data)
-
-    #extract symbol
-    processed.data <- processed.data[, -2]
-
     progress$set(0.33, message = "Calculating plot")
 
-    #plot
+    # generate groups from selection
+    if (is.null(factor_data()$label)) {
+      factor <- ""
+    } else {
+      factor <- factor_data()$label
+    }
+    grouping <- data.table::data.table(object()$metadata[key %in% selector$selectedColumns(), key], factor)
+
+    # plot
     plot <- create_geneview(
-      data = processed.data,
-      grouping = metadata.r()[level == selector$type() & key %in% selector$selectedColumns(), c(1, 2)],
+      data = if (object()$get_uniqueID() == object()$get_name()) result.data()$data[, -2] else result.data()$data, # without name column
+      grouping = grouping,
       plot.type = input$plotType,
       facet.target = input$groupby,
       facet.cols = input$plotColumns,
@@ -304,50 +251,15 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
     return(plot)
   })
 
-  #enable plot button only if plot possible
-  shiny::observe({
-    if(is.null(input$genes) | length(selector$selectedColumns()) < 1){
-      shinyjs::disable("plot")
-    }else if(input$plotType == "violin"){
-      factor1.levels <- metadata.r()[level == selector$type() & key %in% selector$selectedColumns() & factor1 != ""][, .N, keyby = factor1][["N"]]
-
-      if(input$groupby == "condition"){
-        #every level >= 3 times
-        factor1.levels <- ifelse(length(factor1.levels) > 0, factor1.levels, FALSE)
-        if(all(factor1.levels >= 3)){
-          shinyjs::enable("plot")
-        }else{
-          shinyjs::disable("plot")
-        }
-      }else if(input$groupby == "gene"){
-        #at least one level >= 3 times
-        if(any(factor1.levels >= 3)){
-          shinyjs::enable("plot")
-        }else{
-          shinyjs::disable("plot")
-        }
-      }
-    }else{
-      shinyjs::enable("plot")
-    }
-  })
-
-  output$geneView <- shiny::renderUI({
-    if(plot.method == "interactive"){
-      shinycssloaders::withSpinner(plotly::plotlyOutput(session$ns("interactive")), proxy.height = "800px")
-    }else if (plot.method == "static"){
-      shinycssloaders::withSpinner(shiny::plotOutput(session$ns("static")), proxy.height = "800px")
-    }
-  })
-
-  if(plot.method == "interactive") {
+  # render plot ######
+  if (plot.method == "interactive") {
     output$interactive <- plotly::renderPlotly({
-      if(clearPlot()) {
+      if (clearPlot()) {
         return()
       } else {
         log_message("GeneView: render plot interactive", "INFO", token = session$token)
 
-        #progress indicator
+        # progress indicator
         progress <- shiny::Progress$new()
         on.exit(progress$close())
         progress$set(message = "Rendering plot", value = 0)
@@ -358,17 +270,17 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
         return(plot)
       }
     })
-  } else if(plot.method == "static") {
+  } else if (plot.method == "static") {
     output$static <- shiny::renderPlot(
       width = shiny::reactive(plot()$width * (plot()$ppi / 2.54)),
       height = shiny::reactive(plot()$height * (plot()$ppi / 2.54)),
       {
-        if(clearPlot()) {
+        if (clearPlot()) {
           return()
         } else {
           log_message("GeneView: render plot static", "INFO", token = session$token)
 
-          #progress indicator
+          # progress indicator
           progress <- shiny::Progress$new()
           on.exit(progress$close())
           progress$set(message = "Rendering plot", value = 0.3)
@@ -381,6 +293,7 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
       })
   }
 
+  # download #####
   output$download <- shiny::downloadHandler(filename = "geneView.zip",
                                             content = function(file) {
                                               log_message("GeneView: download", "INFO", token = session$token)
@@ -394,15 +307,12 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
     data <- list(
       genes = input$genes,
       columns = list(type = selector$type(), selectedColumns = selector$selectedColumns()),
+      group = factor_data()$selected,
       groupby = input$groupby
     )
 
     # format options
-    if(!is.null(custom.label)) {
-      label <- custom_label()$selected
-    } else {
-      label <- NULL
-    }
+    label <- custom_label()$selected
     options <- list(
       plot_type = input$plotType,
       transformation = transform$method(),
@@ -417,22 +327,88 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
     all <- list(data = data, options = options)
   })
 
+  # notifications #####
+  # enable plot button only if plot possible
+  shiny::observe({
+    if (is.null(input$genes) || !shiny::isTruthy(selector$selectedColumns())) {
+      shinyjs::disable("plot")
+    }else if (input$plotType == "violin") {
+      factor_levels <- table(droplevels(as.factor(factor_data()$label), exclude = ""))
+
+      if (input$groupby == "condition") {
+        # every level >= 3 times
+        factor_levels <- ifelse(length(factor_levels) > 0, factor_levels, FALSE)
+        if (all(factor_levels >= 3)) {
+          shinyjs::enable("plot")
+        } else {
+          shinyjs::disable("plot")
+        }
+      } else if (input$groupby == "gene") {
+        # at least one level >= 3 times
+        if (any(factor_levels >= 3)) {
+          shinyjs::enable("plot")
+        } else {
+          shinyjs::disable("plot")
+        }
+      }
+    } else {
+      shinyjs::enable("plot")
+    }
+  })
+
+  # warning for heavy computation
+  shiny::observe({
+    shiny::req(input$genes)
+
+    if (length(input$genes) > 50) {
+      shiny::showNotification(
+        paste("Caution! You selected", length(input$genes), "genes. This may take a while to compute."),
+        duration = 5,
+        type = "warning",
+        id = "warning",
+        closeButton = FALSE
+      )
+    }else{
+      shiny::removeNotification("warning")
+    }
+  })
+
+  # warning if plot size exceeds limits
+  shiny::observe({
+    if (plot()$exceed_size) {
+      shiny::showNotification(
+        ui = "Width and/ or height exceed limit. Using 500 cm instead.",
+        id = "limit",
+        type = "warning"
+      )
+    } else {
+      shiny::removeNotification("limit")
+    }
+  })
+  # Fetch the reactive guide for this module
+  guide <- geneViewGuide(session)
+  shiny::observeEvent(input$guide, {
+    rintrojs::introjs(session, options = list(steps = guide()))
+  })
+
   return(shiny::reactive(result.data()$data))
 }
 
 #' geneView module guide
 #'
 #' @param session The shiny session
-#' @param label Boolean to show custom label step.
 #'
 #' @return A shiny reactive that contains the texts for the Guide steps.
 #'
-geneViewGuide <- function(session, label = FALSE) {
+geneViewGuide <- function(session) {
   steps <- list(
     "guide_geneSelection" = "<h4>Gene selection</h4>
       Select genes to be displayed.",
+    "guide_genelabel" = "<h4>Custom label</h4>
+      Select one or more columns to be used as a label instead of the names above.",
     "guide_columnSelection" = "<h4>Column selection</h4>
       First select a column type for visualization, then select individual columns from all columns of the chosen type.<br/>
+      Second select grouping factor(s). 'None' will result in no grouping, multiple selection in a single merged factor.<br/>
       After that choose a factor by which the given subset is grouped. E.g. 'condition' will generate a plot for each condition or uses the conditions as x-axis ticks, based on the choosen plot type.",
     "guide_type" = "<h4>Plot type</h4>
       Choose the preferred type of plot that will be rendered.",
@@ -451,11 +427,5 @@ geneViewGuide <- function(session, label = FALSE) {
       As a final step, a click on the 'Plot' button will render the plot, while a click on the 'Reset' button will reset the parameters to default."
   )
 
-  if(label) {
-    steps <- append(steps, values = list("guide_genelabel" = "<h4>Custom label</h4>
-      Select one or more columns to be used as a label instead of the names above."),
-                    after = 1)
-  }
-
   shiny::reactive(data.frame(element = paste0("#", session$ns(names(steps))), intro = unlist(steps)))
 }
diff --git a/exec/geneView_example.R b/exec/geneView_example.R
index 10fac4a..2def399 100644
--- a/exec/geneView_example.R
+++ b/exec/geneView_example.R
@@ -9,12 +9,14 @@ source("../R/columnSelector.R")
 source("../R/label.R")
 source("../R/limit.R")
 source("../R/global.R")
+source("../R/clarion.R")
 
-####Test Data
-data <- data.table::data.table(id = rownames(mtcars), names = rownames(mtcars), mtcars)
+# test data
+data <- data.table::as.data.table(mtcars, keep.rowname = "id")
 # create metadata
-metadata <- data.table::data.table(names(data), factor1 = rep("", length.out = length(names(data))), level = c(rep("annotation", 2), rep("performance", 7), rep("design", 4)))
+metadata <- data.table::data.table(names(data), level = c("feature", rep("sample", 7), rep("condition", 4)))
 names(metadata)[1] <- "key"
+clarion <- Clarion$new(data = data, metadata = metadata)
 ####
 
 ui <- dashboardPage(header = dashboardHeader(), sidebar = dashboardSidebar(
@@ -26,17 +28,7 @@ ui <- dashboardPage(header = dashboardHeader(), sidebar = dashboardSidebar(
 )))
 
 server <- function(input, output) {
-  table.r <- reactive({
-    data
-  })
-  metadata.r <- reactive({
-    metadata
-  })
-  level.r <- reactive({
-    metadata[level != "annotation"][["level"]]
-  })
-
-  gene <- callModule(geneView, "id", data = table.r, metadata.r, level.r, custom.label = table.r, plot.method = "static", width = reactive(input$width), height = reactive(input$height), scale = reactive(input$scale))
+  gene <- callModule(geneView, "id", clarion = clarion, plot.method = "static", width = reactive(input$width), height = reactive(input$height), scale = reactive(input$scale))
 
   observe({
     print(gene())
diff --git a/man/geneView.Rd b/man/geneView.Rd
index b8e755d..a9852c2 100644
--- a/man/geneView.Rd
+++ b/man/geneView.Rd
@@ -4,9 +4,9 @@
 \alias{geneView}
 \title{geneView's module server logic}
 \usage{
-geneView(input, output, session, data, metadata, level = NULL,
-  plot.method = "static", custom.label = NULL, label.sep = ", ",
-  width = "auto", height = "auto", ppi = 72, scale = 1)
+geneView(input, output, session, clarion, plot.method = "static",
+  label.sep = ", ", width = "auto", height = "auto", ppi = 72,
+  scale = 1)
 }
 \arguments{
 \item{input}{Shiny's input object.}
@@ -15,22 +15,10 @@ geneView(input, output, session, data, metadata, level = NULL,
 
 \item{session}{Shiny's session object.}
 
-\item{data}{data.table:
-column1   : ids
-column2   : symbol (data used for selection)
-column3-n : data}
-
-\item{metadata}{data.table:
-column1: ids
-column2: factor1 (conditions)
-column3: level (condition type)}
-
-\item{level}{Vector containing data levels to select from (default: unique(metadata[["level"]])).}
+\item{clarion}{A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)}
 
 \item{plot.method}{Choose which method is used for plotting. Either "static" or "interactive" (Default = "static").}
 
-\item{custom.label}{Data.table used for creating custom labels (supports reactive).}
-
 \item{label.sep}{Seperator used for label merging (Default = ", ").}
 
 \item{width}{Width of the plot in cm. Defaults to minimal size for readable labels and supports reactive.}
diff --git a/man/geneViewGuide.Rd b/man/geneViewGuide.Rd
index 8470d5e..dab0b44 100644
--- a/man/geneViewGuide.Rd
+++ b/man/geneViewGuide.Rd
@@ -4,12 +4,10 @@
 \alias{geneViewGuide}
 \title{geneView module guide}
 \usage{
-geneViewGuide(session, label = FALSE)
+geneViewGuide(session)
 }
 \arguments{
 \item{session}{The shiny session}
-
-\item{label}{Boolean to show custom label step.}
 }
 \value{
 A shiny reactive that contains the texts for the Guide steps.

From 0331d8bca596179d6781bfe406b689e0b99abf9f Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 9 May 2018 08:54:52 +0200
Subject: [PATCH 10/75] geneview: fixed wrong if

---
 R/geneView.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/geneView.R b/R/geneView.R
index 5d9964a..bf45a95 100644
--- a/R/geneView.R
+++ b/R/geneView.R
@@ -230,7 +230,7 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
 
     # plot
     plot <- create_geneview(
-      data = if (object()$get_uniqueID() == object()$get_name()) result.data()$data[, -2] else result.data()$data, # without name column
+      data = if (object()$get_uniqueID() == object()$get_name()) result.data()$data else result.data()$data[, -2], # without name column
       grouping = grouping,
       plot.type = input$plotType,
       facet.target = input$groupby,

From a72e328fc98adb5b36ccf479baf866c954b40251 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 9 May 2018 08:55:19 +0200
Subject: [PATCH 11/75] geneview_example: added factors

---
 exec/geneView_example.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/exec/geneView_example.R b/exec/geneView_example.R
index 2def399..5a17273 100644
--- a/exec/geneView_example.R
+++ b/exec/geneView_example.R
@@ -14,7 +14,7 @@ source("../R/clarion.R")
 # test data
 data <- data.table::as.data.table(mtcars, keep.rowname = "id")
 # create metadata
-metadata <- data.table::data.table(names(data), level = c("feature", rep("sample", 7), rep("condition", 4)))
+metadata <- data.table::data.table(names(data), level = c("feature", rep("sample", 7), rep("condition", 4)), factor1 = c(rep("a", 5), rep("b", 7)), factor2 = c(rep("1", 7), rep("2", 5)), factor3 = c(rep("", 4), rep("test", 5), rep("test2", 3)))
 names(metadata)[1] <- "key"
 clarion <- Clarion$new(data = data, metadata = metadata)
 ####

From 7fd4753dbb293d400b56191203055bbb74e522e6 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 9 May 2018 11:19:04 +0200
Subject: [PATCH 12/75] columnSelector: fixed sub_label used as label if no
 label provided

---
 R/columnSelector.R            | 71 +++++++++++++++++++----------------
 exec/columnSelector_example.R |  3 +-
 man/columnSelector.Rd         |  8 ++--
 3 files changed, 44 insertions(+), 38 deletions(-)

diff --git a/R/columnSelector.R b/R/columnSelector.R
index 528de10..bfd3f99 100644
--- a/R/columnSelector.R
+++ b/R/columnSelector.R
@@ -26,10 +26,10 @@ columnSelectorUI <- function(id, label = F, title = NULL) {
 #' @param output Shiny's output object
 #' @param session Shiny's session object
 #' @param type.columns data.table: (Supports reactive)
-#'                                column1 = columnnames (id)
-#'                                column2 = type (datalevel)
-#'                                column3 = label (optional, used instead of id)
-#'                                column4 = sub_label (optional, added to id/ label)
+#'                                key = columnnames (id)
+#'                                level = datalevel/ type of column
+#'                                label = optional, used instead of id
+#'                                sub_label = optional, added to id/ label
 #' @param type The type (contrast/group/sample of the type dropdown menu, selected in step 1 (upper dropdown). Defaults to unique(type.columns[,2]) (Supports reactive)
 #' @param columnTypeLabel Changes the label of the first UI element
 #' @param labelLabel Change label above label text input.
@@ -42,27 +42,27 @@ columnSelectorUI <- function(id, label = F, title = NULL) {
 #'
 #' @export
 columnSelector <- function(input, output, session, type.columns, type = NULL, columnTypeLabel = "Type of Column", labelLabel = "Label", multiple = TRUE, none = FALSE, sep = ", ", suffix = NULL) {
-  #handle reactive input
+  # handle reactive input
   type.columns.r <- shiny::reactive({
-    if(shiny::is.reactive(type.columns)){
+    if (shiny::is.reactive(type.columns)) {
       type.columns()
-    }else{
+    } else {
       type.columns
     }
   })
   type.r <- shiny::reactive({
-    if(!is.null(type)){
-      if(shiny::is.reactive(type)){
+    if (!is.null(type)) {
+      if (shiny::is.reactive(type)) {
         type()
-      }else{
+      } else {
         type
       }
-    }else{
+    } else {
       unique(type.columns.r()[[2]])
     }
   })
   suffix.r <- shiny::reactive({
-    if(shiny::is.reactive(suffix)) {
+    if (shiny::is.reactive(suffix)) {
       suffix()
     } else {
       suffix
@@ -70,13 +70,13 @@ columnSelector <- function(input, output, session, type.columns, type = NULL, co
   })
 
   output$out <- shiny::renderUI({
-    if(none){
-      choices <- c("None", type.columns.r()[type.columns.r()[[2]] %in% type.r()[1]][[1]])
+    if (none) {
+      choices <- c("None", type.columns.r()[type.columns.r()[["level"]] %in% type.r()[1]][["key"]])
     }else{
-      choices <- type.columns.r()[type.columns.r()[[2]] %in% type.r()[1]][[1]]
+      choices <- type.columns.r()[type.columns.r()[["level"]] %in% type.r()[1]][["key"]]
     }
     columnSelectLabel = "Select individual column"
-    if(multiple) {
+    if (multiple) {
       columnSelectLabel = paste0(columnSelectLabel, "(s)")
     }
 
@@ -86,27 +86,33 @@ columnSelector <- function(input, output, session, type.columns, type = NULL, co
     )
   })
 
-  #show label textInput
+  # show label textInput
   output$showLabel <- shiny::renderUI({
     shiny::textInput(session$ns("select.label"), label = labelLabel)
   })
 
   # make label
   create_label <- shiny::reactive({
-    if(ncol(type.columns.r()) > 2) {
+    shiny::req(input$select.type)
+    # empty label on 'None'
+    if (none && input$select.column == "None") return("")
+
+    if (is.element("label", names(type.columns.r()))) {
       label_id <- input$select.column
-      label_label <- type.columns.r()[type.columns.r()[[1]] %in% input$select.column][[3]]
+      label_label <- type.columns.r()[type.columns.r()[["key"]] %in% input$select.column][["label"]]
 
       # replace id with label
       label <- ifelse(label_label == "", label_id, label_label)
 
-      if(ncol(type.columns.r()) > 3) {
-        label <- paste(label, type.columns.r()[type.columns.r()[[1]] %in% input$select.column][[4]])
-      }
     } else {
       label <- input$select.column
     }
 
+    # add sub_label
+    if (is.element("sub_label", names(type.columns.r()))) {
+      label <- paste(label, type.columns.r()[type.columns.r()[["key"]] %in% input$select.column][["sub_label"]])
+    }
+
     label <- paste(label, collapse = sep)
 
     return(label)
@@ -118,8 +124,8 @@ columnSelector <- function(input, output, session, type.columns, type = NULL, co
     suffix.r()
 
     shiny::isolate({
-      if(!is.null(input$select.label)) {
-        if(!multiple && !is.null(suffix.r())) {
+      if (!is.null(input$select.label)) {
+        if (!multiple && !is.null(suffix.r())) {
           value <- paste(create_label(), suffix.r(), sep = sep)
         } else {
           value <- create_label()
@@ -129,27 +135,27 @@ columnSelector <- function(input, output, session, type.columns, type = NULL, co
     })
   })
 
-  #show columns based on selected type
+  # show columns based on selected type
   shiny::observe({
-    if(none){
-      columns <- c("None", type.columns.r()[type.columns.r()[[2]] %in% input$select.type][[1]])
-    }else{
-      columns <- type.columns.r()[type.columns.r()[[2]] %in% input$select.type][[1]]
+    if (none) {
+      columns <- c("None", type.columns.r()[type.columns.r()[["level"]] %in% input$select.type][["key"]])
+    } else {
+      columns <- type.columns.r()[type.columns.r()[["level"]] %in% input$select.type][["key"]]
     }
 
     shiny::updateSelectizeInput(session = session, inputId = "select.column", choices = columns)
   })
 
   out.type <- shiny::reactive(input$select.type)
-  out.selectedColumns <- shiny::reactive(if(shiny::isTruthy(input$select.column) && input$select.column != "None") input$select.column else "")
+  out.selectedColumns <- shiny::reactive(if (shiny::isTruthy(input$select.column) && input$select.column != "None") input$select.column else "")
   out.label <- shiny::reactive({
-    if(is.null(input$select.label)) {
+    if (is.null(input$select.label)) {
       label <- create_label()
     } else {
       label <- input$select.label
     }
 
-    if(multiple) {
+    if (multiple) {
       label <- unlist(strsplit(label, split = sep, fixed = TRUE))
     }
 
@@ -157,5 +163,4 @@ columnSelector <- function(input, output, session, type.columns, type = NULL, co
   })
 
   return(list(type = out.type, selectedColumns = out.selectedColumns, label = out.label))
-
 }
diff --git a/exec/columnSelector_example.R b/exec/columnSelector_example.R
index 004144b..6609afc 100644
--- a/exec/columnSelector_example.R
+++ b/exec/columnSelector_example.R
@@ -2,7 +2,8 @@ library(shiny)
 source("../R/columnSelector.R")
 
 ###Test Data
-table <- data.table::data.table(names = c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j"), type = c("sample", "codition", "contrast"))
+table <- data.table::data.table(id = c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j"), level = c("sample", "condition", "contrast"), sub_label = "sub")
+names(table)[1] <- "key"
 
 ui <- fluidPage(
   fluidRow(
diff --git a/man/columnSelector.Rd b/man/columnSelector.Rd
index 886804c..8f785aa 100644
--- a/man/columnSelector.Rd
+++ b/man/columnSelector.Rd
@@ -16,10 +16,10 @@ columnSelector(input, output, session, type.columns, type = NULL,
 \item{session}{Shiny's session object}
 
 \item{type.columns}{data.table: (Supports reactive)
-column1 = columnnames (id)
-column2 = type (datalevel)
-column3 = label (optional, used instead of id)
-column4 = sub_label (optional, added to id/ label)}
+key = columnnames (id)
+level = datalevel/ type of column
+label = optional, used instead of id
+sub_label = optional, added to id/ label}
 
 \item{type}{The type (contrast/group/sample of the type dropdown menu, selected in step 1 (upper dropdown). Defaults to unique(type.columns[,2]) (Supports reactive)}
 

From b5ab1808e4de2fff0e44713e403faf97a2b5a0f0 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 9 May 2018 11:24:54 +0200
Subject: [PATCH 13/75] global_cor_heatmap: use clarion object

---
 R/global_cor_heatmap.R            | 99 ++++++++++++++-----------------
 exec/global_cor_heatmap_example.R |  7 ++-
 man/global_cor_heatmap.Rd         | 13 +---
 3 files changed, 53 insertions(+), 66 deletions(-)

diff --git a/R/global_cor_heatmap.R b/R/global_cor_heatmap.R
index 974ed50..5c51f72 100644
--- a/R/global_cor_heatmap.R
+++ b/R/global_cor_heatmap.R
@@ -147,35 +147,37 @@ global_cor_heatmapUI <- function(id) {
 #' @param input Shiny's input object
 #' @param output Shiny's output object
 #' @param session Shiny's session object
-#' @param data data.table data visualized in plot (supports reactive).
-#' @param types data.table: (supports reactive)
-#'                        column1: colnames of data
-#'                        column2: corresponding column type
-#'                        column3 = label (optional, used instead of id)
-#'                        column4 = sub_label (optional, added to id/ label)
+#' @param clarion A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)
 #' @param plot.method Choose which method is used for plotting. Either "static" or "interactive" (Default = "static").
 #' @param width Width of the plot in cm. Defaults to minimal size for readable labels and supports reactive.
 #' @param height Height of the plot in cm. Defaults to minimal size for readable labels and supports reactive.
 #' @param ppi Pixel per inch. Defaults to 72 and supports reactive.
 #' @param scale Scale plot size. Defaults to 1, supports reactive.
 #'
-#'
-#'
 #' @return Reactive containing data used for plotting.
 #'
 #' @export
-global_cor_heatmap <- function(input, output, session, data, types, plot.method = "static", width = "auto", height = "auto", ppi = 72, scale = 1) {
+global_cor_heatmap <- function(input, output, session, clarion, plot.method = "static", width = "auto", height = "auto", ppi = 72, scale = 1) {
+  # globals -----------------------------------------------------------------
+  # clear plot
+  clearPlot <- shiny::reactiveVal(FALSE)
+  # disable downloadButton on init
+  shinyjs::disable("download")
+
   # load module -------------------------------------------------------------
-  # handle reactive data
-  data_r <- shiny::reactive({
-    if(shiny::is.reactive(data)) {
-      data <- data.table::copy(data())
-    }else {
-      data <- data.table::copy(data)
-    }
+  object <- shiny::reactive({
+    # support reactive
+    if (shiny::is.reactive(clarion)) {
+      if (!methods::is(clarion(), "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
+
+      obj <- clarion()$clone(deep = TRUE)
+    } else {
+      if (!methods::is(clarion, "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-    return(data)
+      obj <- clarion$clone(deep = TRUE)
+    }
   })
+
   # handle reactive sizes
   size <- shiny::reactive({
     width <- ifelse(shiny::is.reactive(width), width(), width)
@@ -183,17 +185,17 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
     ppi <- ifelse(shiny::is.reactive(ppi), ppi(), ppi)
     scale <- ifelse(shiny::is.reactive(scale), scale(), scale)
 
-    if(!is.numeric(width) || width <= 0) {
+    if (!is.numeric(width) || width <= 0) {
       width <- "auto"
     }
-    if(!is.numeric(height) || height <= 0) {
-      if(plot.method == "interactive") {
+    if (!is.numeric(height) || height <= 0) {
+      if (plot.method == "interactive") {
         height <- 28
-      }else {
+      } else {
         height <- "auto"
       }
     }
-    if(!is.numeric(ppi) || ppi <= 0) {
+    if (!is.numeric(ppi) || ppi <= 0) {
       ppi <- 72
     }
 
@@ -204,25 +206,22 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
   })
 
   # load internal modules
-  columns <- shiny::callModule(columnSelector, "select", type.columns = types, columnTypeLabel = "Column types to choose from")
-  transform <- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(data_r()[, columns$selectedColumns(), with = FALSE])))
+  columns <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
+  transform <- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selectedColumns(), with = FALSE])))
   colorPicker <- shiny::callModule(colorPicker2, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(result_data()[, -1])))
 
   # load dynamic ui
-  if(plot.method == "static") {
+  if (plot.method == "static") {
     output$cor_heatmap <- shiny::renderUI({
       shinycssloaders::withSpinner(shiny::plotOutput(outputId = session$ns("static")), proxy.height = "800px")
     })
-  }else if(plot.method == "interactive") {
+  } else if (plot.method == "interactive") {
     output$cor_heatmap <- shiny::renderUI({
       shinycssloaders::withSpinner(plotly::plotlyOutput(outputId = session$ns("interactive")), proxy.height = "800px")
     })
   }
 
   # functionality -----------------------------------------------------------
-  # clear plot
-  clearPlot <- shiny::reactiveVal(FALSE)
-
   # reset ui
   shiny::observeEvent(input$reset, {
     log_message("Global correlation heatmap: reset", "INFO", token = session$token)
@@ -235,15 +234,15 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
     shinyjs::reset("label")
     shinyjs::reset("row_label")
     shinyjs::reset("column_label")
-    columns <<- shiny::callModule(columnSelector, "select", type.columns = types, columnTypeLabel = "Column types to choose from")
-    transform <<- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(data_r()[, columns$selectedColumns(), with = FALSE])))
+    columns <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
+    transform <<- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selectedColumns(), with = FALSE])))
     colorPicker <<- shiny::callModule(colorPicker2, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(result_data()[, -1])))
     clearPlot(TRUE)
   })
 
   # warning if plot size exceeds limits
   shiny::observe({
-    if(plot()$exceed_size) {
+    if (plot()$exceed_size) {
       shiny::showNotification(
         ui = "Width and/ or height exceed limit. Using 500 cm instead.",
         id = "limit",
@@ -264,7 +263,7 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
   shiny::observe({
     shiny::req(columns$selectedColumns())
 
-    if(length(columns$selectedColumns()) < 2) {
+    if (length(columns$selectedColumns()) < 2) {
       shiny::showNotification(
         ui = "Warning! At least two columns needed. Please select more.",
         id = "less_data_warning",
@@ -277,7 +276,7 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
 
   # enable/ disable plot button
   shiny::observe({
-    if(!shiny::isTruthy(columns$selectedColumns()) || length(columns$selectedColumns()) < 2) {
+    if (!shiny::isTruthy(columns$selectedColumns()) || length(columns$selectedColumns()) < 2) {
       shinyjs::disable("plot")
     }else {
       shinyjs::enable("plot")
@@ -291,10 +290,10 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
 
   # show right methods
   shiny::observe({
-    if(input$calc == "distance") {
+    if (input$calc == "distance") {
       shiny::updateSelectInput(session = session, inputId = "calc_method",
                                choices = c("euclidean", "maximum", "manhattan", "canberra", "minkowski"))
-    }else if(input$calc == "correlation") {
+    } else if (input$calc == "correlation") {
       shiny::updateSelectInput(session = session, inputId = "calc_method", choices = c("spearman", "pearson", "kendall"))
     }
   })
@@ -307,16 +306,11 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
     on.exit(progress$close())
     progress$set(0.2, message = "Compute data")
 
-    # process data
-    processed_data <- data.table::as.data.table(transform$data())
-    processed_data <- processed_data[, columns$selectedColumns(), with = FALSE]
-    processed_data <- data.table::data.table(data_r()[, 1], processed_data)
-
     # corellate data
-    if(input$calc == "distance") {
-      processed_data <- data.table::as.data.table(as.matrix(stats::dist(t(processed_data[, -1]), method = input$calc_method)), keep.rownames = "Names")
-    }else if(input$calc == "correlation") {
-      processed_data <- data.table::as.data.table(stats::cor(processed_data[, -1], method = input$calc_method), keep.rownames = "Names")
+    if (input$calc == "distance") {
+      processed_data <- data.table::as.data.table(as.matrix(stats::dist(t(transform$data()), method = input$calc_method)), keep.rownames = "Names")
+    } else if (input$calc == "correlation") {
+      processed_data <- data.table::as.data.table(stats::cor(transform$data(), method = input$calc_method), keep.rownames = "Names")
     }
 
     # update progress indicator
@@ -325,9 +319,6 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
     return(processed_data)
   })
 
-  # disable downloadButton on init
-  shinyjs::disable("download")
-
   # build plot object
   plot <- shiny::eventReactive(input$plot, {
     log_message("Global correlation heatmap: computing plot...", "INFO", token = session$token)
@@ -343,12 +334,12 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
     progress$set(0.2, message = "Building plot")
 
     # check if rlog failed
-    if(is.null(attr(transform$data(), "betaPriorVar")) && is.null(attr(transform$data(), "intercept")) && transform$method() == "rlog") {
+    if (is.null(attr(transform$data(), "betaPriorVar")) && is.null(attr(transform$data(), "intercept")) && transform$method() == "rlog") {
       shiny::showNotification("Regularized log failed (dispersion within 2 orders of magnitude)! Performing log2 instead.",
                               duration = 5,
                               type = "warning")
 
-      if(input$label == "rlog") {
+      if (input$label == "rlog") {
         unitlabel <- "log2"
         shiny::updateTextInput(session = session, inputId = "label", value = unitlabel)
       } else {
@@ -386,12 +377,12 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
   })
 
   # render plot
-  if(plot.method == "static") {
+  if (plot.method == "static") {
     output$static <- shiny::renderPlot(
       width = shiny::reactive(plot()$width * (plot()$ppi / 2.54)),
       height = shiny::reactive(plot()$height * (plot()$ppi / 2.54)),
       {
-        if(clearPlot()) {
+        if (clearPlot()) {
           return()
         } else {
           log_message("Global correlation heatmap: render plot static", "INFO", token = session$token)
@@ -412,9 +403,9 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
         }
       }
     )
-  }else if(plot.method == "interactive") {
+  } else if (plot.method == "interactive") {
     output$interactive <- plotly::renderPlotly({
-      if(clearPlot()) {
+      if (clearPlot()) {
         return()
       } else {
         log_message("Global correlation heatmap: render plot interactive", "INFO", token = session$token)
diff --git a/exec/global_cor_heatmap_example.R b/exec/global_cor_heatmap_example.R
index 215865a..9a43f15 100644
--- a/exec/global_cor_heatmap_example.R
+++ b/exec/global_cor_heatmap_example.R
@@ -7,12 +7,15 @@ source("../R/transformation.R")
 source("../R/global_cor_heatmap.R")
 source("../R/limit.R")
 source("../R/global.R")
+source("../R/clarion.R")
 
 # test data
 data <- data.table::as.data.table(mtcars, keep.rowname = "id")
 # create metadata
-metadata <- data.table::data.table(names(data), type = c("annotation", rep("performance", 7), rep("design", 4)))
+metadata <- data.table::data.table(names(data), level = c("feature", rep("sample", 7), rep("condition", 4)))
 names(metadata)[1] <- "key"
+clarion <- Clarion$new(data = data, metadata = metadata)
+#####
 
 ui <- dashboardPage(
   header = dashboardHeader(),
@@ -29,7 +32,7 @@ ui <- dashboardPage(
 )
 
 server <- function(input, output) {
-  table <- shiny::callModule(global_cor_heatmap, "id", data = data, types = metadata[type %in% c("performance", "design")], plot.method = "static", width = reactive(input$width), height = reactive(input$height), scale = reactive(input$scale))
+  table <- shiny::callModule(global_cor_heatmap, "id", clarion = clarion, plot.method = "static", width = reactive(input$width), height = reactive(input$height), scale = reactive(input$scale))
 
   shiny::observe({
     print(table())
diff --git a/man/global_cor_heatmap.Rd b/man/global_cor_heatmap.Rd
index 80e86b8..cf0d13e 100644
--- a/man/global_cor_heatmap.Rd
+++ b/man/global_cor_heatmap.Rd
@@ -4,9 +4,8 @@
 \alias{global_cor_heatmap}
 \title{global correlation heatmap module server logic}
 \usage{
-global_cor_heatmap(input, output, session, data, types,
-  plot.method = "static", width = "auto", height = "auto", ppi = 72,
-  scale = 1)
+global_cor_heatmap(input, output, session, clarion, plot.method = "static",
+  width = "auto", height = "auto", ppi = 72, scale = 1)
 }
 \arguments{
 \item{input}{Shiny's input object}
@@ -15,13 +14,7 @@ global_cor_heatmap(input, output, session, data, types,
 
 \item{session}{Shiny's session object}
 
-\item{data}{data.table data visualized in plot (supports reactive).}
-
-\item{types}{data.table: (supports reactive)
-column1: colnames of data
-column2: corresponding column type
-column3 = label (optional, used instead of id)
-column4 = sub_label (optional, added to id/ label)}
+\item{clarion}{A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)}
 
 \item{plot.method}{Choose which method is used for plotting. Either "static" or "interactive" (Default = "static").}
 

From 776aeb9777040023a201fca810b7ccea6e130f4a Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 9 May 2018 15:07:21 +0200
Subject: [PATCH 14/75] heatmap: use clarion object

---
 R/heatmap.R            | 253 +++++++++++++++++++----------------------
 exec/heatmap_example.R |  15 +--
 man/heatmap.Rd         |  16 +--
 man/heatmapGuide.Rd    |   4 +-
 4 files changed, 128 insertions(+), 160 deletions(-)

diff --git a/R/heatmap.R b/R/heatmap.R
index dccdacc..c0a279b 100644
--- a/R/heatmap.R
+++ b/R/heatmap.R
@@ -91,14 +91,8 @@ heatmapUI <- function(id, row.label = TRUE) {
 #' @param input Shiny's input object
 #' @param output Shiny's output object
 #' @param session Shiny's session object
-#' @param data data.table data visualized in plot (Supports reactive).
-#' @param types data.table: (Supports reactive)
-#'                        column1: colnames of data
-#'                        column2: corresponding column typ
-#'                        column3: label (optional, used instead of id)
-#'                        column4: sub_label (optional, added to id/ label)
+#' @param clarion A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)
 #' @param plot.method Choose which method is used for plotting. Either "static" or "interactive" (Default = "static").
-#' @param custom.row.label Data.table used for creating custom labels (supports reactive).
 #' @param label.sep Seperator used for label merging (Default = ", ").
 #' @param width Width of the plot in cm. Defaults to minimal size for readable labels and supports reactive.
 #' @param height Height of the plot in cm. Defaults to minimal size for readable labels and supports reactive.
@@ -108,19 +102,30 @@ heatmapUI <- function(id, row.label = TRUE) {
 #' @return Reactive containing data used for plotting.
 #'
 #' @export
-heatmap <- function(input, output, session, data, types, plot.method = "static", custom.row.label = NULL, label.sep = ", ", width = "auto", height = "auto", ppi = 72, scale = 1) {
+heatmap <- function(input, output, session, clarion, plot.method = "static", label.sep = ", ", width = "auto", height = "auto", ppi = 72, scale = 1) {
+  # globals/ initialization #####
   # cluster limitation
   static <- 11000
   interactive <- 3000
+  # clear plot
+  clearPlot <- shiny::reactiveVal(FALSE)
+  # disable downloadButton on init
+  shinyjs::disable("download")
 
-  #handle reactive data
-  data.r <- shiny::reactive({
-    if(shiny::is.reactive(data)){
-      data <- data.table::copy(data())
-    }else{
-      data <- data.table::copy(data)
+  # input preparation #####
+  object <- shiny::reactive({
+    # support reactive
+    if (shiny::is.reactive(clarion)) {
+      if (!methods::is(clarion(), "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
+
+      obj <- clarion()$clone(deep = TRUE)
+    } else {
+      if (!methods::is(clarion, "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
+
+      obj <- clarion$clone(deep = TRUE)
     }
   })
+
   # handle reactive sizes
   size <- shiny::reactive({
     width <- ifelse(shiny::is.reactive(width), width(), width)
@@ -128,17 +133,17 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
     ppi <- ifelse(shiny::is.reactive(ppi), ppi(), ppi)
     scale <- ifelse(shiny::is.reactive(scale), scale(), scale)
 
-    if(!is.numeric(width) || width <= 0) {
+    if (!is.numeric(width) || width <= 0) {
       width <- "auto"
     }
-    if(!is.numeric(height) || height <= 0) {
-      if(plot.method == "interactive") {
+    if (!is.numeric(height) || height <= 0) {
+      if (plot.method == "interactive") {
         height <- 28
-      }else {
+      } else {
         height <- "auto"
       }
     }
-    if(!is.numeric(ppi) || ppi <= 0) {
+    if (!is.numeric(ppi) || ppi <= 0) {
       ppi <- 72
     }
 
@@ -148,69 +153,18 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
          scale = scale)
   })
 
-  # Fetch the reactive guide for this module
-  guide <- heatmapGuide(session, !is.null(custom.row.label))
-  shiny::observeEvent(input$guide, {
-    rintrojs::introjs(session, options = list(steps = guide()))
-  })
-
-  #notification
-  shiny::observe({
-    shiny::req(data.r())
-
-    if(shiny::isTruthy(columns$selectedColumns())){
-      if(input$clustering != "none") { # clustering
-        if(plot.method == "static" && nrow(data.r()) > static) { # cluster limitation (static)
-          shiny::showNotification(
-            paste("Clustering limited to", static, "genes! Please disable clustering or select less genes."),
-            duration = NULL,
-            type = "error",
-            id = session$ns("notification"),
-            closeButton = FALSE
-          )
-        } else if(plot.method == "interactive" && nrow(data.r()) > interactive) { # cluster limitation (interactive)
-          shiny::showNotification(
-            paste("Clustering limited to", interactive, "genes! Please disable clustering or select less genes."),
-            duration = NULL,
-            type = "error",
-            id = session$ns("notification"),
-            closeButton = FALSE
-          )
-        } else {
-          shiny::removeNotification(session$ns("notification"))
-        }
-      } else if(nrow(data.r()) > 200) { # computation warning
-        shiny::showNotification(
-          paste("Caution! You selected", nrow(data.r()), "genes. This will take a while to compute."),
-          duration = 5,
-          type = "warning",
-          id = session$ns("notification"),
-          closeButton = FALSE
-        )
-      } else {
-        shiny::removeNotification(session$ns("notification"))
-      }
-    }else{
-      shiny::removeNotification(session$ns("notification"))
-    }
-  })
+  # modules/ ui #####
+  columns <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
+  transform <- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selectedColumns(), with = FALSE])))
+  colorPicker <- shiny::callModule(colorPicker2, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(transform$data())))
+  custom_label <- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data), label = "Select row label", sep = label.sep, disable = shiny::reactive(!input$row.label))
 
-  # warning if plot size exceeds limits
+  # automatic unitlabel
   shiny::observe({
-    if(plot()$exceed_size) {
-      shiny::showNotification(
-        ui = "Width and/ or height exceed limit. Using 500 cm instead.",
-        id = "limit",
-        type = "warning"
-      )
-    } else {
-      shiny::removeNotification("limit")
-    }
+    shiny::updateTextInput(session = session, inputId = "label", value = transform$method())
   })
 
-  # clear plot
-  clearPlot <- shiny::reactiveVal(FALSE)
-
+  # functionality/ plotting #####
   # reset ui
   shiny::observeEvent(input$reset, {
     log_message("Heatmap: reset", "INFO", token = session$token)
@@ -222,39 +176,25 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
     shinyjs::reset("label")
     shinyjs::reset("row.label")
     shinyjs::reset("column.label")
-    columns <<- shiny::callModule(columnSelector, "select", type.columns = types, columnTypeLabel = "Column types to choose from")
-    transform <<- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(data.r()[, columns$selectedColumns(), with = FALSE])))
+    columns <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
+    transform <<- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selectedColumns(), with = FALSE])))
     colorPicker <<- shiny::callModule(colorPicker2, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(transform$data())))
-    if(!is.null(custom.row.label)) {
-      custom_label <<- shiny::callModule(label, "labeller", data = custom.row.label, label = "Select row label", sep = label.sep, disable = shiny::reactive(!input$row.label))
-    }
+    custom_label <<- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data), label = "Select row label", sep = label.sep, disable = shiny::reactive(!input$row.label))
     clearPlot(TRUE)
   })
 
-  columns <- shiny::callModule(columnSelector, "select", type.columns = types, columnTypeLabel = "Column types to choose from")
-  transform <- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(data.r()[, columns$selectedColumns(), with = FALSE])))
-  colorPicker <- shiny::callModule(colorPicker2, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(transform$data())))
-  if(!is.null(custom.row.label)) {
-    custom_label <- shiny::callModule(label, "labeller", data = custom.row.label, label = "Select row label", sep = label.sep, disable = shiny::reactive(!input$row.label))
-  }
-
   result.data <- shiny::eventReactive(input$plot, {
-    #new progress indicator
+    # new progress indicator
     progress <- shiny::Progress$new()
     on.exit(progress$close())
     progress$set(0.2, message = "Compute data")
 
-    processed_data <- data.table::as.data.table(transform$data())
-
-    processed_data <- data.table::data.table(data.r()[, 1], processed_data)
+    processed_data <- data.table::data.table(object()$data[, object()$get_uniqueID(), with = FALSE], transform$data())
 
     progress$set(1)
     return(processed_data)
   })
 
-  # disable downloadButton on init
-  shinyjs::disable("download")
-
   plot <- shiny::eventReactive(input$plot, {
     log_message("Heatmap: computing plot...", "INFO", token = session$token)
 
@@ -262,30 +202,22 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
     shinyjs::enable("download")
     clearPlot(FALSE)
 
-    #new progress indicator
+    # new progress indicator
     progress <- shiny::Progress$new()
     on.exit(progress$close())
     progress$set(0.2, message = "Compute plot")
 
-    colors <- colorPicker()$palette
-
-    if(!is.null(custom.row.label)) {
-      label <- custom_label()$label
-    } else {
-      label <- NULL
-    }
-
     plot <- create_heatmap(
       data = result.data(),
       unitlabel = input$label,
       row.label = input$row.label,
-      row.custom.label = label,
+      row.custom.label = custom_label()$label,
       column.label = input$column.label,
       column.custom.label = make.unique(columns$label()),
       clustering = input$clustering,
       clustdist = input$cluster.distance,
       clustmethod = input$cluster.method,
-      colors = colors,
+      colors = colorPicker()$palette,
       width = size()$width,
       height = size()$height,
       ppi = size()$ppi,
@@ -300,19 +232,19 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
     return(plot)
   })
 
-  #render choosen plotUI
-  if(plot.method == "interactive"){
+  # render plot #####
+  if (plot.method == "interactive") {
     output$heatmap <- shiny::renderUI({
       shinycssloaders::withSpinner(plotly::plotlyOutput(session$ns("interactive")), proxy.height = "800px")
     })
 
     output$interactive <- plotly::renderPlotly({
-      if(clearPlot()) {
+      if (clearPlot()) {
         return()
       } else {
         log_message("Heatmap: render plot interactive", "INFO", token = session$token)
 
-        #new progress indicator
+        # new progress indicator
         progress <- shiny::Progress$new()
         on.exit(progress$close())
         progress$set(0.2, message = "Render plot")
@@ -324,7 +256,7 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
         return(plot)
       }
     })
-  }else{
+  } else {
     output$heatmap <- shiny::renderUI({
       shinycssloaders::withSpinner(shiny::plotOutput(session$ns("static")), proxy.height = "800px")
     })
@@ -333,12 +265,12 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
       width = shiny::reactive(plot()$width * (plot()$ppi / 2.54)),
       height = shiny::reactive(plot()$height * (plot()$ppi / 2.54)),
       {
-        if(clearPlot()) {
+        if (clearPlot()) {
           return()
         } else {
           log_message("Heatmap: render plot static", "INFO", token = session$token)
 
-          #new progress indicator
+          # new progress indicator
           progress <- shiny::Progress$new()
           on.exit(progress$close())
           progress$set(0.2, message = "Render plot")
@@ -346,7 +278,7 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
           plot <- plot()$plot
 
           # handle error
-          if(methods::is(plot, "try-error")) {
+          if (methods::is(plot, "try-error")) {
             # TODO add logging
             stop("An error occured! Please try a different dataset.")
           }
@@ -357,6 +289,8 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
     })
   }
 
+
+  # download #####
   output$download <- shiny::downloadHandler(filename = "heatmap.zip",
                                             content = function(file) {
                                               log_message("Heatmap: download", "INFO", token = session$token)
@@ -364,7 +298,6 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
                                               download(file = file, filename = "heatmap.zip", plot = plot()$plot, width = plot()$width, height = plot()$height, ppi = plot()$ppi, ui = user_input())
                                             })
 
-
   user_input <- shiny::reactive({
     # format selection
     selection <- list(type = columns$type(), selectedColumns = columns$selectedColumns())
@@ -390,6 +323,7 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
     all <- list(selection = selection, clustering = clustering, options = options)
   })
 
+  # notifications #####
   # enable/ disable plot button
   # show warning if disabled
   shiny::observe({
@@ -397,26 +331,26 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
     show_warning <- TRUE
 
     # are columns selected?
-    if(shiny::isTruthy(columns$selectedColumns())) {
-      row.num <- nrow(shiny::isolate(data.r()))
+    if (shiny::isTruthy(columns$selectedColumns())) {
+      row.num <- nrow(shiny::isolate(object()$data))
       col.num <- length(columns$selectedColumns())
 
       # minimal heatmap possible (greater 1x1)?
-      if(row.num > 1 || col.num > 1) {
+      if (row.num > 1 || col.num > 1) {
         # no clustering for single rows or columns
-        if(row.num == 1 && !is.element(input$clustering, c("both", "row"))) {
+        if (row.num == 1 && !is.element(input$clustering, c("both", "row"))) {
           show_warning <- FALSE
           shinyjs::enable("plot")
-        } else if(col.num == 1 && !is.element(input$clustering, c("both", "column"))) {
+        } else if (col.num == 1 && !is.element(input$clustering, c("both", "column"))) {
           show_warning <- FALSE
           shinyjs::enable("plot")
-        } else if(row.num > 1 && col.num > 1) { # no border case heatmaps
+        } else if (row.num > 1 && col.num > 1) { # no border case heatmaps
           show_warning <- FALSE
           shinyjs::enable("plot")
         }
       }
 
-      if(show_warning) {
+      if (show_warning) {
         shiny::showNotification(
           ui = "Warning! Insufficient columns/ rows. Either disable the respective clustering or expand the dataset.",
           id = "insuf_data",
@@ -427,15 +361,70 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
       }
 
       # maximum heatmap reached?
-      if(plot.method == "static" && row.num > static || plot.method == "interactive" && row.num > interactive) {
+      if (plot.method == "static" && row.num > static || plot.method == "interactive" && row.num > interactive) {
         shinyjs::disable("plot")
       }
     }
   })
 
-  # automatic unitlabel
+  # cluster limitation
   shiny::observe({
-    shiny::updateTextInput(session = session, inputId = "label", value = transform$method())
+    shiny::req(object())
+
+    if (shiny::isTruthy(columns$selectedColumns())) {
+      if (input$clustering != "none") { # clustering
+        if (plot.method == "static" && nrow(object()$data) > static) { # cluster limitation (static)
+          shiny::showNotification(
+            paste("Clustering limited to", static, "genes! Please disable clustering or select less genes."),
+            duration = NULL,
+            type = "error",
+            id = session$ns("notification"),
+            closeButton = FALSE
+          )
+        } else if (plot.method == "interactive" && nrow(object()$data) > interactive) { # cluster limitation (interactive)
+          shiny::showNotification(
+            paste("Clustering limited to", interactive, "genes! Please disable clustering or select less genes."),
+            duration = NULL,
+            type = "error",
+            id = session$ns("notification"),
+            closeButton = FALSE
+          )
+        } else {
+          shiny::removeNotification(session$ns("notification"))
+        }
+      } else if (nrow(object()$data) > 200) { # computation warning
+        shiny::showNotification(
+          paste("Caution! You selected", nrow(object()$data), "genes. This will take a while to compute."),
+          duration = 5,
+          type = "warning",
+          id = session$ns("notification"),
+          closeButton = FALSE
+        )
+      } else {
+        shiny::removeNotification(session$ns("notification"))
+      }
+    } else {
+      shiny::removeNotification(session$ns("notification"))
+    }
+  })
+
+  # warning if plot size exceeds limits
+  shiny::observe({
+    if (plot()$exceed_size) {
+      shiny::showNotification(
+        ui = "Width and/ or height exceed limit. Using 500 cm instead.",
+        id = "limit",
+        type = "warning"
+      )
+    } else {
+      shiny::removeNotification("limit")
+    }
+  })
+
+  # Fetch the reactive guide for this module
+  guide <- heatmapGuide(session)
+  shiny::observeEvent(input$guide, {
+    rintrojs::introjs(session, options = list(steps = guide()))
   })
 
   return(result.data)
@@ -444,11 +433,10 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
 #' heatmap module guide
 #'
 #' @param session The shiny session
-#' @param custom.row.label Boolean. Show additional info. Default = FALSE.
 #'
 #' @return A shiny reactive that contains the texts for the Guide steps.
 #'
-heatmapGuide <- function(session, custom.row.label = FALSE) {
+heatmapGuide <- function(session) {
   steps <- list(
     "guide_selection" = "<h4>Data selection</h4>
       Select a column type for visualization, then select individual columns based on the chosen type.",
@@ -462,14 +450,11 @@ heatmapGuide <- function(session, custom.row.label = FALSE) {
       The selected palette can additionally be reversed.<br/>
       Set the limits of the color palette with 'Winsorize to upper/lower'. Out of bounds values will be mapped to the nearest color.",
     "guide_options" = "<h4>Additional options</h4>
-      You can set a label for the color legend that describes the underlying data unit. Furthermore, you can enable/disable row and column labels.",
+      You can set a label for the color legend that describes the underlying data unit. Furthermore, you can enable/disable row and column labels.
+      Use the input to generate custom row-labels. The selected columns will be merged and used as label.",
     "guide_buttons" = "<h4>Create the plot</h4>
       As a final step click, a click on the 'Plot' button will render the plot, while a click on the 'Reset' button will reset the parameters to default."
   )
 
-  if(custom.row.label) {
-    steps[["guide_options"]] <- paste(steps[["guide_options"]], "Use the input to generate custom row-labels. The selected columns will be merged and used as label.")
-  }
-
   shiny::reactive(data.frame(element = paste0("#", session$ns(names(steps))), intro = unlist(steps)))
 }
diff --git a/exec/heatmap_example.R b/exec/heatmap_example.R
index 6f65148..e15d6fe 100644
--- a/exec/heatmap_example.R
+++ b/exec/heatmap_example.R
@@ -1,4 +1,3 @@
-
 library(shiny)
 library(shinydashboard)
 source("../R/function.R")
@@ -9,12 +8,14 @@ source("../R/heatmap.R")
 source("../R/label.R")
 source("../R/limit.R")
 source("../R/global.R")
+source("../R/clarion.R")
 
 ####Test Data
 data <- data.table::as.data.table(mtcars, keep.rowname = "id")
 # create metadata
-metadata <- data.table::data.table(names(data), type = c("annotation", rep("performance", 7), rep("design", 4)))
+metadata <- data.table::data.table(names(data), level = c("feature", rep("sample", 7), rep("condition", 4)))
 names(metadata)[1] <- "key"
+clarion <- Clarion$new(data = data, metadata = metadata)
 ####
 
 
@@ -27,15 +28,7 @@ ui <- dashboardPage(header = dashboardHeader(), sidebar = dashboardSidebar(
 )))
 
 server <- function(input, output) {
-  table <- reactive({
-    data
-  })
-  typ <- reactive({
-    # without annotation
-    metadata[ type != "annotation"]
-  })
-
-  heat <- callModule(heatmap, "id", data = table, types = typ, plot.method = "interactive", custom.row.label = table, width = reactive(input$width), height = reactive(input$height), scale = reactive(input$scale))
+  heat <- callModule(heatmap, "id", clarion = clarion, plot.method = "interactive", width = reactive(input$width), height = reactive(input$height), scale = reactive(input$scale))
 
   observe({
     print(heat())
diff --git a/man/heatmap.Rd b/man/heatmap.Rd
index 077dbf4..a54c357 100644
--- a/man/heatmap.Rd
+++ b/man/heatmap.Rd
@@ -4,9 +4,9 @@
 \alias{heatmap}
 \title{heatmap module server logic}
 \usage{
-heatmap(input, output, session, data, types, plot.method = "static",
-  custom.row.label = NULL, label.sep = ", ", width = "auto",
-  height = "auto", ppi = 72, scale = 1)
+heatmap(input, output, session, clarion, plot.method = "static",
+  label.sep = ", ", width = "auto", height = "auto", ppi = 72,
+  scale = 1)
 }
 \arguments{
 \item{input}{Shiny's input object}
@@ -15,18 +15,10 @@ heatmap(input, output, session, data, types, plot.method = "static",
 
 \item{session}{Shiny's session object}
 
-\item{data}{data.table data visualized in plot (Supports reactive).}
-
-\item{types}{data.table: (Supports reactive)
-column1: colnames of data
-column2: corresponding column typ
-column3: label (optional, used instead of id)
-column4: sub_label (optional, added to id/ label)}
+\item{clarion}{A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)}
 
 \item{plot.method}{Choose which method is used for plotting. Either "static" or "interactive" (Default = "static").}
 
-\item{custom.row.label}{Data.table used for creating custom labels (supports reactive).}
-
 \item{label.sep}{Seperator used for label merging (Default = ", ").}
 
 \item{width}{Width of the plot in cm. Defaults to minimal size for readable labels and supports reactive.}
diff --git a/man/heatmapGuide.Rd b/man/heatmapGuide.Rd
index b5b6967..207ec23 100644
--- a/man/heatmapGuide.Rd
+++ b/man/heatmapGuide.Rd
@@ -4,12 +4,10 @@
 \alias{heatmapGuide}
 \title{heatmap module guide}
 \usage{
-heatmapGuide(session, custom.row.label = FALSE)
+heatmapGuide(session)
 }
 \arguments{
 \item{session}{The shiny session}
-
-\item{custom.row.label}{Boolean. Show additional info. Default = FALSE.}
 }
 \value{
 A shiny reactive that contains the texts for the Guide steps.

From d7ef90935c9e5124cc202da587e3c6b7f8a76acd Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Mon, 14 May 2018 10:15:40 +0200
Subject: [PATCH 15/75] pca: use clarion object

---
 R/pca.R            | 232 +++++++++++++++++++++------------------------
 exec/pca_example.R |   8 +-
 man/pca.Rd         |  16 +---
 3 files changed, 117 insertions(+), 139 deletions(-)

diff --git a/R/pca.R b/R/pca.R
index 249af4f..5cdc603 100644
--- a/R/pca.R
+++ b/R/pca.R
@@ -66,14 +66,7 @@ pcaUI <- function(id, show.label = TRUE) {
 #' @param input Shiny's input object
 #' @param output Shiny's output object
 #' @param session Shiny's session object
-#' @param data data.table data visualized in plot. (Supports Reactive)
-#' @param types data.table: (Supports reactive)
-#'                        column1: colnames of data
-#'                        column2: corresponding column typ
-#'                        column3: label (optional, used instead of id)
-#'                        column4: sub_label (optional, added to id/ label)
-#' @param levels Levels from which data is selected (Defaults to unique(metadata[["level"]])). (Supports Reactive)
-#' @param entryLabel Define additional columns added to each entry (Default = NULL). Use a vector containing the desired columnnames e.g. c("column1", "column2").
+#' @param clarion A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)
 #' @param width Width of the plot in cm. Defaults to 28 and supports reactive.
 #' @param height Height of the plot in cm. Defaults to 28 and supports reactive.
 #' @param ppi Pixel per inch. Defaults to 72 and supports reactive.
@@ -86,38 +79,26 @@ pcaUI <- function(id, show.label = TRUE) {
 #' @import data.table
 #'
 #' @export
-pca <- function(input, output, session, data, types, levels = NULL, entryLabel = NULL, width = 28, height = 28, ppi = 72, scale = 1) {
-  #handle reactive data
-  data.r <- shiny::reactive({
-    if(shiny::is.reactive(data)){
-      data <- data.table::copy(data())
-    }else{
-      data <- data.table::copy(data)
-    }
-    #merge columns for additional label info
-    if(!is.null(entryLabel)){
-      data[, 1 := apply(data[, c(names(data)[1], entryLabel), with = FALSE], 1, paste, collapse = ", ")]
-      names(data)[1] <- paste(names(data)[1], paste(entryLabel, collapse = ", "), sep = ", ")
-    }
+pca <- function(input, output, session, clarion, width = 28, height = 28, ppi = 72, scale = 1) {
+  # globals/ initialization #####
+  # clear plot
+  clearPlot <- shiny::reactiveVal(value = FALSE)
+  # disable downloadButton on init
+  shinyjs::disable("download")
+  # disable plot button on init
+  shinyjs::disable("plot")
 
-    return(data)
-  })
-  types.r <- shiny::reactive({
-    if(shiny::is.reactive(types)){
-      types()
-    }else{
-      types
-    }
-  })
-  levels.r <- shiny::reactive({
-    if(is.null(levels)){
-      metadata.r()[["level"]]
-    }else{
-      if(shiny::is.reactive(levels)){
-        levels()
-      }else{
-        levels
-      }
+  # input preparation #####
+  object <- shiny::reactive({
+    # support reactive
+    if (shiny::is.reactive(clarion)) {
+      if (!methods::is(clarion(), "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
+
+      obj <- clarion()$clone(deep = TRUE)
+    } else {
+      if (!methods::is(clarion, "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
+
+      obj <- clarion$clone(deep = TRUE)
     }
   })
 
@@ -128,13 +109,13 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
     ppi <- ifelse(shiny::is.reactive(ppi), ppi(), ppi)
     scale <- ifelse(shiny::is.reactive(scale), scale(), scale)
 
-    if(!is.numeric(width) | width <= 0) {
+    if (!is.numeric(width) | width <= 0) {
       width <- 28
     }
-    if(!is.numeric(height) | height <= 0) {
+    if (!is.numeric(height) | height <= 0) {
       height <- 28
     }
-    if(!is.numeric(ppi) | ppi <= 0) {
+    if (!is.numeric(ppi) | ppi <= 0) {
       ppi <- 72
     }
 
@@ -144,16 +125,24 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
          scale = scale)
   })
 
+  # modules/ ui #####
+  columnSelect <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
 
-  guide <- pcaGuide(session)
-  shiny::observeEvent(input$guide, {
-    rintrojs::introjs(session, options = list(steps = guide()))
-  })
+  # update dimension inputs
+  shiny::observe({
+    col_num <- length(shiny::req(columnSelect$selectedColumns()))
 
-  # clear plot
-  clearPlot <- shiny::reactiveVal(value = FALSE)
+    if (col_num >= 3) {
+      valueA <- ifelse(col_num <= input$dimA, col_num - 1, input$dimA)
+      valueB <- ifelse(col_num <= input$dimB, col_num - 1, input$dimB)
+
+      shiny::updateNumericInput(session = session, inputId = "dimA", max = col_num - 1, value = valueA)
+      shiny::updateNumericInput(session = session, inputId = "dimB", max = col_num - 1, value = valueB)
+    }
+  })
 
-  #reset ui
+  # functionality/ plotting #####
+  # reset ui
   shiny::observeEvent(input$reset, {
     log_message("PCA: reset", "INFO", token = session$token)
 
@@ -162,80 +151,24 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
     shinyjs::reset("dimB")
     shinyjs::reset("pointsize")
     shinyjs::reset("labelsize")
-    columnSelect <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(types.r()[level %in% levels.r(), c("key", "level"), with = FALSE]), columnTypeLabel = "Column types to choose from")
+    columnSelect <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
     clearPlot(TRUE)
   })
 
-  columnSelect <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(types.r()[level %in% levels.r(), c("key", "level"), with = FALSE]), columnTypeLabel = "Column types to choose from")
-
-  output$datalevel <- shiny::renderUI({
-    shiny::selectInput(session$ns("select"), label = "select data level", choices = unique(levels.r()))
-  })
-
-  # disable plot button on init
-  shinyjs::disable("plot")
-  # update dimension inputs
-  shiny::observe({
-    col.num <- length(shiny::req(columnSelect$selectedColumns()))
-
-    if(col.num < 3 || nrow(shiny::isolate(data.r())) < 3 || is.na(input$dimA) || is.na(input$dimB)){
-      shinyjs::disable("plot")
-
-      # show warning if not enough selected
-      shiny::showNotification(
-        ui = "Not enough columns/ rows selected! At least 3 of each needed for plotting.",
-        id = "warning",
-        type = "warning"
-      )
-    }else{
-      shiny::removeNotification("warning")
-      shinyjs::enable("plot")
-
-      if(col.num <= input$dimA){
-        valueA <- col.num - 1
-      }else{
-        valueA <- input$dimA
-      }
-      if(col.num <= input$dimB){
-        valueB <- col.num - 1
-      }else{
-        valueB <- input$dimB
-      }
-      shiny::updateNumericInput(inputId = "dimA", session = session, max = col.num - 1, value = valueA)
-      shiny::updateNumericInput(inputId = "dimB", session = session, max = col.num - 1, value = valueB)
-    }
-  })
-
-  # warning if plot size exceeds limits
-  shiny::observe({
-    if(computed.data()$exceed_size) {
-      shiny::showNotification(
-        ui = "Width and/ or height exceed limit. Using 500 cm instead.",
-        id = "limit",
-        type = "warning"
-      )
-    } else {
-      shiny::removeNotification("limit")
-    }
-  })
-
-  selected <- shiny::reactive({
+  result_data <- shiny::reactive({
     #new progress indicator
     progress <- shiny::Progress$new()
     on.exit(progress$close())
     progress$set(0.2, message = "Select data")
 
-    selected <- data.r()[, c(names(data.r())[1], columnSelect$selectedColumns()), with = FALSE]
+    selected <- object()$data[, c(object()$get_uniqueID(), columnSelect$selectedColumns()), with = FALSE]
 
     progress$set(1)
 
     return(selected)
   })
 
-  # disable downloadButton on init
-  shinyjs::disable("download")
-
-  computed.data <- shiny::eventReactive(input$plot, {
+  plot <- shiny::eventReactive(input$plot, {
     log_message("PCA: computing plot...", "INFO", token = session$token)
 
     # enable downloadButton
@@ -248,7 +181,7 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
     progress$set(0.2, message = "Render plot")
 
     plot <- create_pca(
-               data = selected(),
+               data = result_data(),
                dimensionA = input$dimA,
                dimensionB = input$dimB,
                dimensions = length(columnSelect$selectedColumns()) - 1,
@@ -267,21 +200,19 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
 
     log_message("PCA: done.", "INFO", token = session$token)
 
-    # show plot
-    shinyjs::show("pca")
-
     return(plot)
   })
 
+  # render plot #####
   # get width in pixel
   plot_width <- shiny::reactive({
-    width <- computed.data()$width * (computed.data()$ppi / 2.54)
+    width <- plot()$width * (plot()$ppi / 2.54)
     ifelse(width < 50, 50, width)
   })
 
   # get height in pixel
   plot_height <- shiny::reactive({
-    height <- computed.data()$height * (computed.data()$ppi / 2.54)
+    height <- plot()$height * (plot()$ppi / 2.54)
     ifelse(height < 50, 50, height)
   })
 
@@ -289,28 +220,29 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
     width = plot_width,
     height = plot_height,
     {
-      if(clearPlot()){
+      if (clearPlot()) {
         return()
       } else {
         log_message("PCA: render plot", "INFO", token = session$token)
 
-        computed.data()$plot
+        plot()$plot
       }
     })
 
-  #group data by dimension
-  reorganized.data <- shiny::reactive({
-    sapply(colnames(computed.data()$data$var$coord), USE.NAMES = TRUE, simplify = FALSE, function(dim) {
-      sapply(computed.data()$data$var, function(table) {
+  # group data by dimension
+  reorganized_data <- shiny::reactive({
+    sapply(colnames(plot()$data$var$coord), USE.NAMES = TRUE, simplify = FALSE, function(dim) {
+      sapply(plot()$data$var, function(table) {
         table[, dim]
       })
     })
   })
 
+  # download #####
   output$download <- shiny::downloadHandler(filename = "pca.zip",
                                             content = function(file) {
                                               log_message("PCA: download", "INFO", token = session$token)
-                                              download(file = file, filename = "pca.zip", plot = computed.data()$plot, width = plot_width() / (computed.data()$ppi / 2.54), height = plot_height() / (computed.data()$ppi / 2.54), ppi = computed.data()$ppi, ui = user_input())
+                                              download(file = file, filename = "pca.zip", plot = plot()$plot, width = plot_width() / (plot()$ppi / 2.54), height = plot_height() / (plot()$ppi / 2.54), ppi = plot()$ppi, ui = user_input())
                                             })
 
   user_input <- shiny::reactive({
@@ -331,7 +263,61 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
     all <- list(selection = selection, options = options)
   })
 
-  return(reorganized.data)
+  # notifications #####
+  # insufficient data/ invalid dimension warnings
+  shiny::observe({
+    shinyjs::enable("plot")
+
+    col_num <- length(shiny::req(columnSelect$selectedColumns()))
+
+    # invalid dimension
+    if (col_num >= 3 && (is.na(input$dimA) || is.na(input$dimB) || input$dimA <= 0 || input$dimA >= col_num || input$dimB <= 0 || input$dimB >= col_num)) {
+      shinyjs::disable("plot")
+
+      shiny::showNotification(
+        ui = "Invalid dimension(s)! Please select an integer value between 1 and number of selected columns - 1.",
+        id = "dimension",
+        type = "warning"
+      )
+    } else {
+      shiny::removeNotification("dimension")
+    }
+
+    # insufficient data
+    if (col_num < 3 || nrow(shiny::isolate(object()$data)) < 3) {
+      shinyjs::disable("plot")
+
+      shiny::showNotification(
+        ui = "Not enough columns/ rows selected! At least 3 of each needed for plotting.",
+        id = "data",
+        type = "warning"
+      )
+
+
+    } else {
+      shiny::removeNotification("data")
+    }
+  })
+
+  # warning if plot size exceeds limits
+  shiny::observe({
+    if (plot()$exceed_size) {
+      shiny::showNotification(
+        ui = "Width and/ or height exceed limit. Using 500 cm instead.",
+        id = "limit",
+        type = "warning"
+      )
+    } else {
+      shiny::removeNotification("limit")
+    }
+  })
+
+  guide <- pcaGuide(session)
+  shiny::observeEvent(input$guide, {
+    rintrojs::introjs(session, options = list(steps = guide()))
+  })
+
+  return(reorganized_data)
 }
 
 #' pca module guide
diff --git a/exec/pca_example.R b/exec/pca_example.R
index 107a5b8..7299b69 100644
--- a/exec/pca_example.R
+++ b/exec/pca_example.R
@@ -5,12 +5,14 @@ source("../R/columnSelector.R")
 source("../R/function.R")
 source("../R/pca.R")
 source("../R/global.R")
+source("../R/clarion.R")
 
-#### Test Data
+####Test Data
 data <- data.table::as.data.table(mtcars, keep.rowname = "id")
 # create metadata
-metadata <- data.table::data.table(names(data), level = c("annotation", rep("performance", 7), rep("design", 4)))
+metadata <- data.table::data.table(names(data), level = c("feature", rep("sample", 7), rep("condition", 4)))
 names(metadata)[1] <- "key"
+clarion <- Clarion$new(data = data, metadata = metadata)
 ####
 
 ui <- dashboardPage(header = dashboardHeader(), sidebar = dashboardSidebar(
@@ -22,7 +24,7 @@ ui <- dashboardPage(header = dashboardHeader(), sidebar = dashboardSidebar(
 )))
 
 server <- function(input, output) {
-  callModule(pca, "id", data = data, types = metadata, levels = metadata[level != "annotation"][["level"]], width = reactive(input$width), height = reactive(input$height), scale = reactive(input$scale))
+  callModule(pca, "id", clarion = clarion, width = reactive(input$width), height = reactive(input$height), scale = reactive(input$scale))
 }
 
 # Run the application
diff --git a/man/pca.Rd b/man/pca.Rd
index eee0778..4d7571a 100644
--- a/man/pca.Rd
+++ b/man/pca.Rd
@@ -4,8 +4,8 @@
 \alias{pca}
 \title{pca module server logic}
 \usage{
-pca(input, output, session, data, types, levels = NULL, entryLabel = NULL,
-  width = 28, height = 28, ppi = 72, scale = 1)
+pca(input, output, session, clarion, width = 28, height = 28, ppi = 72,
+  scale = 1)
 }
 \arguments{
 \item{input}{Shiny's input object}
@@ -14,17 +14,7 @@ pca(input, output, session, data, types, levels = NULL, entryLabel = NULL,
 
 \item{session}{Shiny's session object}
 
-\item{data}{data.table data visualized in plot. (Supports Reactive)}
-
-\item{types}{data.table: (Supports reactive)
-column1: colnames of data
-column2: corresponding column typ
-column3: label (optional, used instead of id)
-column4: sub_label (optional, added to id/ label)}
-
-\item{levels}{Levels from which data is selected (Defaults to unique(metadata[["level"]])). (Supports Reactive)}
-
-\item{entryLabel}{Define additional columns added to each entry (Default = NULL). Use a vector containing the desired columnnames e.g. c("column1", "column2").}
+\item{clarion}{A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)}
 
 \item{width}{Width of the plot in cm. Defaults to 28 and supports reactive.}
 

From 9e82e827e861e94aed0bc0d2cc428ee7a66906c5 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Mon, 14 May 2018 10:59:47 +0200
Subject: [PATCH 16/75] marker: use clarion object

---
 R/marker.R            | 27 +++++++++++++++++----------
 exec/marker_example.R |  8 +++++---
 man/marker.Rd         |  6 +++---
 3 files changed, 25 insertions(+), 16 deletions(-)

diff --git a/R/marker.R b/R/marker.R
index 359c332..57da4a0 100644
--- a/R/marker.R
+++ b/R/marker.R
@@ -22,26 +22,33 @@ markerUI <- function(id, label = "Highlight/ Label Selected Features"){
 #' @param input Shiny's input object.
 #' @param output Shiny's output object.
 #' @param session Shiny's session object.
-#' @param highlight.labels Data.table from which labels are provided (Supports reactive).
+#' @param clarion A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)
 #'
-#' @return A reactive which contains a named list (highlight, color, labelColumn, label).
+#' @return A reactive which contains a named list (highlight, color, labelColumn, label, clarion).
 #'
 #' @export
-marker <- function(input, output, session, highlight.labels){
-  highlight.labels.r <- shiny::reactive({
-    if(shiny::is.reactive(highlight.labels)){
-      highlight.labels()
-    }else{
-      highlight.labels
+marker <- function(input, output, session, clarion){
+  # input preparation #####
+  object <- shiny::reactive({
+    # support reactive
+    if (shiny::is.reactive(clarion)) {
+      if (!methods::is(clarion(), "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
+
+      obj <- clarion()
+    } else {
+      if (!methods::is(clarion, "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
+
+      obj <- clarion
     }
   })
 
+  # modules #####
   color <- shiny::callModule(colorPicker2, "color")
-  labeller <-  shiny::callModule(label, "label", data = shiny::reactive(highlight.labels.r()), unique = FALSE)
+  labeller <-  shiny::callModule(label, "label", data = shiny::reactive(object()$data), unique = FALSE)
 
   shiny::reactive({
     shiny::req(input$highlight, color()$palette)
 
-    list(highlight = input$highlight, color = color()$palette, labelColumn = labeller()$selected, label = labeller()$label)
+    list(highlight = input$highlight, color = color()$palette, labelColumn = labeller()$selected, label = labeller()$label, clarion = object())
   })
 }
diff --git a/exec/marker_example.R b/exec/marker_example.R
index 42ff0eb..45d455f 100644
--- a/exec/marker_example.R
+++ b/exec/marker_example.R
@@ -3,12 +3,14 @@ library(shiny)
 source("../R/marker.R")
 source("../R/colorPicker2.R")
 source("../R/label.R")
+source("../R/clarion.R")
 
-#### Test Data
+####Test Data
 data <- data.table::as.data.table(mtcars, keep.rowname = "id")
 # create metadata
-metadata <- data.table::data.table(names(data), type = c("annotation", rep("performance", 7), rep("design", 4)))
+metadata <- data.table::data.table(names(data), level = c("feature", rep("sample", 7), rep("condition", 4)))
 names(metadata)[1] <- "key"
+clarion <- Clarion$new(data = data, metadata = metadata)
 ####
 
 ui <- fluidPage(
@@ -18,7 +20,7 @@ ui <- fluidPage(
 
 server <- function(input, output) {
 
-  marker <-callModule(marker, "mark", highlight.labels = data)
+  marker <-callModule(marker, "mark", clarion = clarion)
 
   output$output <- renderPrint({
     marker()
diff --git a/man/marker.Rd b/man/marker.Rd
index c8bf5fb..1a021c7 100644
--- a/man/marker.Rd
+++ b/man/marker.Rd
@@ -4,7 +4,7 @@
 \alias{marker}
 \title{marker module server logic}
 \usage{
-marker(input, output, session, highlight.labels)
+marker(input, output, session, clarion)
 }
 \arguments{
 \item{input}{Shiny's input object.}
@@ -13,10 +13,10 @@ marker(input, output, session, highlight.labels)
 
 \item{session}{Shiny's session object.}
 
-\item{highlight.labels}{Data.table from which labels are provided (Supports reactive).}
+\item{clarion}{A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)}
 }
 \value{
-A reactive which contains a named list (highlight, color, labelColumn, label).
+A reactive which contains a named list (highlight, color, labelColumn, label, clarion).
 }
 \description{
 marker module server logic

From fec6cd5162b088f4aa8825a78532d867ba1c2fa1 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Tue, 15 May 2018 08:24:17 +0200
Subject: [PATCH 17/75] marker_example: added missing source

---
 exec/marker_example.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/exec/marker_example.R b/exec/marker_example.R
index 45d455f..64107ef 100644
--- a/exec/marker_example.R
+++ b/exec/marker_example.R
@@ -3,6 +3,7 @@ library(shiny)
 source("../R/marker.R")
 source("../R/colorPicker2.R")
 source("../R/label.R")
+source("../R/limit.R")
 source("../R/clarion.R")
 
 ####Test Data
@@ -19,7 +20,6 @@ ui <- fluidPage(
 )
 
 server <- function(input, output) {
-
   marker <-callModule(marker, "mark", clarion = clarion)
 
   output$output <- renderPrint({

From 70a17c3f4ae3d894757cd6ffb2f32839bad678cf Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Tue, 15 May 2018 09:53:07 +0200
Subject: [PATCH 18/75] marker: return list of reactives for better performance

---
 R/marker.R            | 16 ++++++++++------
 exec/marker_example.R | 10 ++++++++--
 man/marker.Rd         |  2 +-
 3 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/R/marker.R b/R/marker.R
index 57da4a0..e068dff 100644
--- a/R/marker.R
+++ b/R/marker.R
@@ -24,7 +24,7 @@ markerUI <- function(id, label = "Highlight/ Label Selected Features"){
 #' @param session Shiny's session object.
 #' @param clarion A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)
 #'
-#' @return A reactive which contains a named list (highlight, color, labelColumn, label, clarion).
+#' @return A named list containing reactives (highlight, color, labelColumn, label, clarion).
 #'
 #' @export
 marker <- function(input, output, session, clarion){
@@ -46,9 +46,13 @@ marker <- function(input, output, session, clarion){
   color <- shiny::callModule(colorPicker2, "color")
   labeller <-  shiny::callModule(label, "label", data = shiny::reactive(object()$data), unique = FALSE)
 
-  shiny::reactive({
-    shiny::req(input$highlight, color()$palette)
-
-    list(highlight = input$highlight, color = color()$palette, labelColumn = labeller()$selected, label = labeller()$label, clarion = object())
-  })
+  return(
+    list(
+      highlight = shiny::reactive(input$highlight),
+      color = shiny::reactive(color()$palette),
+      labelColumn = shiny::reactive(labeller()$selected),
+      label = shiny::reactive(labeller()$label),
+      clarion = object
+    )
+  )
 }
diff --git a/exec/marker_example.R b/exec/marker_example.R
index 64107ef..8baf245 100644
--- a/exec/marker_example.R
+++ b/exec/marker_example.R
@@ -20,10 +20,16 @@ ui <- fluidPage(
 )
 
 server <- function(input, output) {
-  marker <-callModule(marker, "mark", clarion = clarion)
+  marker <- callModule(marker, "mark", clarion = clarion)
 
   output$output <- renderPrint({
-    marker()
+    list(
+      highlight = marker$highlight(),
+      color = marker$color(),
+      labelColumn = marker$labelColumn(),
+      label = marker$label(),
+      clarion = marker$clarion()
+    )
   })
 }
 
diff --git a/man/marker.Rd b/man/marker.Rd
index 1a021c7..db5689c 100644
--- a/man/marker.Rd
+++ b/man/marker.Rd
@@ -16,7 +16,7 @@ marker(input, output, session, clarion)
 \item{clarion}{A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)}
 }
 \value{
-A reactive which contains a named list (highlight, color, labelColumn, label, clarion).
+A named list containing reactives (highlight, color, labelColumn, label, clarion).
 }
 \description{
 marker module server logic

From af8d39264d701ca10cde5f4816660ecb720bd713 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 16 May 2018 11:18:29 +0200
Subject: [PATCH 19/75] scatterplot: use clarion object

---
 R/function.R               | 169 +++++++------
 R/scatterPlot.R            | 477 +++++++++++++++++++------------------
 exec/scatterPlot_example.R |  14 +-
 man/create_scatterplot.Rd  |  21 +-
 man/scatterPlot.Rd         |  25 +-
 5 files changed, 351 insertions(+), 355 deletions(-)

diff --git a/R/function.R b/R/function.R
index 778d523..762bb3c 100644
--- a/R/function.R
+++ b/R/function.R
@@ -3,18 +3,19 @@
 #' @param data data.table containing plot data
 #'             column 1: id
 #'             column 2, 3(, 4): x, y(, z)
+#' @param data.labels Vector of labels used for data. Length has to be equal to nrow(data).
 #' @param transparency Set point transparency. See \code{\link[ggplot2]{geom_point}}.
 #' @param pointsize Set point size. See \code{\link[ggplot2]{geom_point}}.
 #' @param labelsize Set label size. See \code{\link[ggplot2]{geom_text}}.
-#' @param colors Vector of colors used for color palette
+#' @param color Vector of colors used for color palette.
 #' @param x_label Label x-Axis
 #' @param y_label Label Y-Axis
 #' @param z_label Label Z-Axis
 #' @param density Boolean value, perform 2d density estimate.
 #' @param line Boolean value, add reference line.
 #' @param categorized Z-Axis (if exists) as categories.
-#' @param highlight.data data.table containing data to highlight.
-#' @param highlight.labels Vector of labels used for highlighted data.
+#' @param highlight.data data.table containing data to highlight. Same structure as data.
+#' @param highlight.labels Vector of labels used for highlighted data. Length has to be equal to nrow(data).
 #' @param highlight.color String with hexadecimal color-code.
 #' @param xlim Numeric vector of two setting min and max limit of x-axis. See \code{\link[ggplot2]{lims}}.
 #' @param ylim Numeric vector of two setting min and max limit of y-axis. See \code{\link[ggplot2]{lims}}.
@@ -30,43 +31,42 @@
 #' @import data.table
 #'
 #' @return Returns list(plot = ggplotly/ ggplot, width, height, ppi, exceed_size).
-create_scatterplot <- function(data, transparency = 1, pointsize = 1, labelsize = 3, colors = NULL, x_label = "", y_label = "", z_label = "", density = T, line = T, categorized = F, highlight.data = NULL, highlight.labels = NULL, highlight.color = "#FF0000", xlim = NULL, ylim = NULL, colorbar.limits = NULL, width = "auto", height = "auto", ppi = 72, plot.method = "static", scale = 1){
+create_scatterplot <- function(data, data.labels = NULL, transparency = 1, pointsize = 1, labelsize = 3, color = NULL, x_label = "", y_label = "", z_label = "", density = T, line = T, categorized = F, highlight.data = NULL, highlight.labels = NULL, highlight.color = "#FF0000", xlim = NULL, ylim = NULL, colorbar.limits = NULL, width = "auto", height = "auto", ppi = 72, plot.method = "static", scale = 1){
   ########## prepare data ##########
-  #set labelnames if needed
+  # set labelnames if needed
   x_label <- ifelse(nchar(x_label), x_label, names(data)[2])
   y_label <- ifelse(nchar(y_label), y_label, names(data)[3])
-  if(ncol(data) >= 4){ z_label <- ifelse(nchar(z_label), z_label, names(data)[4])}
+  if (ncol(data) >= 4) z_label <- ifelse(nchar(z_label), z_label, names(data)[4])
 
-  # make column names unqiue to prevent overwrite
+  # make column names unique to prevent overwrite
   columnnames <- names(data)
   names(data) <- make.unique(columnnames)
-  if(!is.null(highlight.data)) {
+  if (!is.null(highlight.data)) {
     columnnames.highlight <- names(highlight.data)
     names(highlight.data) <- make.unique(columnnames.highlight)
   }
 
-  # get intern columnnames
+  # get internal columnnames
   x_head <- names(data)[2]
   y_head <- names(data)[3]
-  if(ncol(data) >= 4){ z_head <- names(data)[4]}
+  if (ncol(data) >= 4) z_head <- names(data)[4]
 
-  #delete rows where both 0 or at least one NA
+  # delete rows where both 0 or at least one NA
   rows.to.keep.data <- which(as.logical((data[, 2] != 0) + (data[, 3] != 0)))
   data <- data[rows.to.keep.data]
-  if(!is.null(highlight.data)){
+  if (!is.null(highlight.data)) {
     rows.to.keep.high <- which(as.logical((highlight.data[, 2] != 0) + (highlight.data[, 3 != 0])))
     highlight.data <- highlight.data[rows.to.keep.high]
   }
 
-  #delete labels accordingly
-  if(is.null(highlight.data)){
-    highlight.labels <- highlight.labels[rows.to.keep.data]
-  }else{
+  # delete labels accordingly
+  data.labels <- data.labels[rows.to.keep.data]
+  if (!is.null(highlight.data)) {
     highlight.labels <- highlight.labels[rows.to.keep.high]
   }
 
   ########## assemble plot ##########
-  theme1 <- ggplot2::theme (											#no gray background or helper lines
+  theme1 <- ggplot2::theme(											# no gray background or helper lines
     plot.background = ggplot2::element_blank(),
     panel.grid.major = ggplot2::element_blank(),
     panel.grid.minor = ggplot2::element_blank(),
@@ -78,123 +78,123 @@ create_scatterplot <- function(data, transparency = 1, pointsize = 1, labelsize
     axis.title.y = ggplot2::element_text(face = "bold", color = "black", size = 10 * scale),
     plot.title = ggplot2::element_text(face = "bold", color = "black", size = 12 * scale),
     text = ggplot2::element_text(size = 10 * scale)
-    #		legend.background = element_rect(color = "red")			#border color
-    #		legend.key = element_rect("green")						#not working!
+    # legend.background = element_rect(color = "red")			# border color
+    # legend.key = element_rect("green")						# not working!
   )
 
-  ###z-axis exists?
-  if(ncol(data) >= 4){
+  ### z-axis exists?
+  if (ncol(data) >= 4) {
     plot <- ggplot2::ggplot(data = data)
 
-    ###scatter with color axis
-    if(categorized == FALSE){
+    ### scatter with color axis
+    if (!categorized) {
       plot <- plot +
-        ###color_gradient
-        ggplot2::scale_color_gradientn(colors = colors, name = z_label, limits = colorbar.limits, oob = scales::squish)
+        ### color_gradient
+        ggplot2::scale_color_gradientn(colors = color, name = z_label, limits = colorbar.limits, oob = scales::squish)
 
-      ###scatter with categories
-    }else if(categorized == TRUE){
-      #change categorized column to factor
+      ### scatter with categories
+    } else if (categorized == TRUE) {
+      # change categorized column to factor
       data <- data[, (z_head) := as.factor(data[[z_head]])]
 
-      ###categorized plot
+      ### categorized plot
       plot <- plot +
 
-        ggplot2::scale_color_manual (
-          #labels = data[,z_head],
-          values = grDevices::colorRampPalette(colors)(length(unique(data[[z_head]]))), #get color for each value,
-          #breaks = ,
-          drop=FALSE,								#to avoid dropping empty factors
+        ggplot2::scale_color_manual(
+          # labels = data[, z_head],
+          values = grDevices::colorRampPalette(color)(length(unique(data[[z_head]]))), # get color for each value
+          # breaks = ,
+          drop = FALSE,								# to avoid dropping empty factors
           name = z_label
-          #			guide=guide_legend(title="sdsds" )					#legend for points
+          # guide=guide_legend(title="sdsds")					# legend for points
         )
     }
-    #set names
+    # set names
     plot <- plot + ggplot2::aes_(x = as.name(x_head), y = as.name(y_head), color = as.name(z_head))
-  }else{
-    plot <- ggplot2::ggplot(data = data, ggplot2::aes_(x = as.name(x_head),y = as.name(y_head)))
+  } else {
+    plot <- ggplot2::ggplot(data = data, ggplot2::aes_(x = as.name(x_head), y = as.name(y_head)))
   }
 
-  if(density == TRUE){
+  if (density) {
     ### kernel density
-    #plot$layers <- c(stat_density2d(geom="tile", aes(fill=..density..^0.25), n=200, contour=FALSE,) + aes_(fill=as.name(var)), plot$layers)#n=resolution; density less sparse
-    plot <- plot + ggplot2::stat_density2d(geom="tile", ggplot2::aes(fill=..density..^0.25), n=200, contour=FALSE)
-
-    plot <- plot + ggplot2::scale_fill_gradient(low="white", high="black") +
-      #guides(fill=FALSE) +		#remove density legend
+    # plot$layers <- c(stat_density2d(geom = "tile", aes(fill = ..density..^0.25), n=200, contour=FALSE) + aes_(fill = as.name(var)), plot$layers) # n = resolution; density less sparse
+    plot <- plot + ggplot2::stat_density2d(geom = "tile", ggplot2::aes(fill = ..density..^0.25), n = 200, contour = FALSE)
 
-      ggplot2::labs(fill="Density")
+    plot <- plot + ggplot2::scale_fill_gradient(low = "white", high = "black") +
+      # guides(fill=FALSE) +		# remove density legend
+      ggplot2::labs(fill = "Density")
   }
 
-  if(line == TRUE){
+  if (line) {
     ### diagonal line
-    plot <- plot + ggplot2::geom_abline(intercept=0, slope=1)
+    plot <- plot + ggplot2::geom_abline(intercept = 0, slope = 1)
   }
 
   plot <- plot +
-    ggplot2::xlab(x_label) +								#axis labels
+    ggplot2::xlab(x_label) +								# axis labels
     ggplot2::ylab(y_label)
 
   # interactive points with hovertexts
-  if(plot.method == "interactive") {
-    #set hovertext
-    if(ncol(data) >=4){
+  if (plot.method == "interactive") {
+    # set hovertext
+    if (ncol(data) >= 4) {
       hovertext <- paste0("</br>", data[[1]],
                           "</br>", x_label, ": ", data[[x_head]],
                           "</br>", y_label, ": ", data[[y_head]],
                           "</br>", z_label, ": ", data[[z_head]])
-    }else{
+    } else {
       hovertext <- paste0("</br>", data[[1]],
                           "</br>", x_label, ": ", data[[x_head]],
                           "</br>", y_label, ": ", data[[y_head]])
     }
 
-    #set points
+    # set points
+    # color if no z-axis
     plot <- plot + ggplot2::geom_point(size = pointsize * scale, alpha = transparency, ggplot2::aes(text = hovertext))
 
-    if(!is.null(highlight.data)){
-      #set highlighted hovertext
-      if(ncol(data) >=4){
+    if (!is.null(highlight.data)) {
+      # set highlighted hovertext
+      if (ncol(data) >= 4) {
         hovertext.high <- paste0("</br>", highlight.data[[1]],
                                  "</br>", x_label, ": ", highlight.data[[x_head]],
                                  "</br>", y_label, ": ", highlight.data[[y_head]],
                                  "</br>", z_label, ": ", highlight.data[[z_head]])
-      }else{
+      } else {
         hovertext.high <- paste0("</br>", highlight.data[[1]],
                                  "</br>", x_label, ": ", highlight.data[[x_head]],
                                  "</br>", y_label, ": ", highlight.data[[y_head]])
       }
 
-      #set highlighted points
+      # set highlighted points
       plot <- plot + ggplot2::geom_point(size = pointsize * scale, alpha = transparency, inherit.aes = TRUE, data = highlight.data, color = highlight.color, show.legend = FALSE, ggplot2::aes(text = hovertext.high))
     }
   # static points without hovertexts
-  } else if(plot.method == "static") {
+  } else if (plot.method == "static") {
     seed <- Sys.getpid() + Sys.time()
     # set points
     plot <- plot + ggplot2::geom_point(size = pointsize * scale, alpha = transparency)
 
     # set highlighted points
-    if(!is.null(highlight.data)) {
+    if (!is.null(highlight.data)) {
       plot <- plot + ggplot2::geom_point(size = pointsize * scale, alpha = transparency, inherit.aes = TRUE, data = highlight.data, color = highlight.color, show.legend = FALSE)
 
       # set repelling point labels
-      if(!is.null(highlight.labels)) {
+      if (!is.null(highlight.labels)) {
         plot <- plot + ggrepel::geom_label_repel(data = highlight.data, mapping = ggplot2::aes(label = highlight.labels), size = labelsize * scale, color = "black", segment.color = "gray65", force = 2, max.iter = 1000, point.padding = grid::unit(0.1, "lines"), label.size = NA, alpha = 0.5, seed = seed)
         plot <- plot + ggrepel::geom_label_repel(data = highlight.data, mapping = ggplot2::aes(label = highlight.labels), size = labelsize * scale, color = "black", segment.color = "gray65", force = 2, max.iter = 1000, point.padding = grid::unit(0.1, "lines"), label.size = NA, fill = NA, seed = seed)
       }
-    # set repelling labels (for only highlighted points shown)
-    } else if(!is.null(highlight.labels) & length(highlight.labels) == nrow(data)) {
-      plot <- plot + ggrepel::geom_label_repel(data = highlight.data, mapping = ggplot2::aes(label = highlight.labels), size = labelsize * scale, color = "black", segment.color = "gray65", force = 2, max.iter = 1000, point.padding = grid::unit(0.1, "lines"), label.size = NA, alpha = 0.5, seed = seed)
-      plot <- plot + ggrepel::geom_label_repel(data = highlight.data, mapping = ggplot2::aes(label = highlight.labels), size = labelsize * scale, color = "black", segment.color = "gray65", force = 2, max.iter = 1000, point.padding = grid::unit(0.1, "lines"), label.size = NA, fill = NA, seed = seed)
+    # set repelling labels (for data)
+    } else if (!is.null(data.labels)) {
+      plot <- plot + ggrepel::geom_label_repel(mapping = ggplot2::aes(label = data.labels), size = labelsize * scale, color = "black", segment.color = "gray65", force = 2, max.iter = 1000, point.padding = grid::unit(0.1, "lines"), label.size = NA, alpha = 0.5, seed = seed)
+      plot <- plot + ggrepel::geom_label_repel(mapping = ggplot2::aes(label = data.labels), size = labelsize * scale, color = "black", segment.color = "gray65", force = 2, max.iter = 1000, point.padding = grid::unit(0.1, "lines"), label.size = NA, fill = NA, seed = seed)
     }
   }
 
-  #set axis limits
-  if(!is.null(xlim)){
+  # set axis limits
+  if (!is.null(xlim)) {
     plot <- plot + ggplot2::xlim(xlim)
   }
-  if(!is.null(ylim)){
+  if (!is.null(ylim)) {
     plot <- plot + ggplot2::ylim(ylim)
   }
 
@@ -202,18 +202,18 @@ create_scatterplot <- function(data, transparency = 1, pointsize = 1, labelsize
 
 
 
-  #estimate legend width
+  # estimate legend width
   legend.width <- 0
   legend.padding <- 20 # 10 on both sides
   legend.thickness <- 30
-  if(density){
+  if (density) {
     legend.width <- nchar("Density")
   }
-  if(ncol(data) > 3){
+  if (ncol(data) > 3) {
     legend.width <- ifelse(legend.width > nchar(z_label), legend.width, nchar(z_label))
   }
-  if(density | ncol(data) > 3){
-    #estimate tickwidth
+  if (density | ncol(data) > 3) {
+    # estimate tickwidth
     min.tick <- nchar(as.character(min(data[[3]], na.rm = TRUE))) * 8.75
     max.tick <- nchar(as.character(max(data[[3]], na.rm = TRUE))) * 8.75
     legend.thickness <- legend.thickness + ifelse(min.tick < max.tick, max.tick, min.tick)
@@ -222,14 +222,14 @@ create_scatterplot <- function(data, transparency = 1, pointsize = 1, labelsize
     legend.width <- ifelse(legend.width > legend.thickness, legend.width, legend.thickness) + legend.padding
   }
 
-  #set width/ height
-  if(width == "auto"){
+  # set width/ height
+  if (width == "auto") {
     # cm to px
     width <- 28 * (ppi / 2.54) + legend.width
   } else {
     width <- width * (ppi / 2.54)
   }
-  if(height == "auto"){
+  if (height == "auto") {
     # cm to px
     height <- 28 * (ppi / 2.54)
   } else {
@@ -243,25 +243,24 @@ create_scatterplot <- function(data, transparency = 1, pointsize = 1, labelsize
   # size exceeded?
   exceed_size <- FALSE
   limit <- 500 * (ppi / 2.54)
-  if(width > limit) {
+  if (width > limit) {
     exceed_size <- TRUE
     width <- limit
   }
-  if(height > limit) {
+  if (height > limit) {
     exceed_size <- TRUE
     height <- limit
   }
 
-  if(plot.method == "interactive") {
+  if (plot.method == "interactive") {
     plot <- plotly::ggplotly(plot, width = width + legend.width, height = height, tooltip = "text")
 
     # add labels with arrows
-    if(!is.null(highlight.labels)) {
-      if(!is.null(highlight.data)) {
-        plot <- plotly::add_annotations(p = plot, x = highlight.data[[x_head]], y = highlight.data[[y_head]], text = highlight.labels, standoff = pointsize * scale, font = list(size = labelsize * scale), bgcolor = 'rgba(255, 255, 255, 0.5)')
-      } else if(nrow(data) == length(highlight.labels)) {
-        plot <- plotly::add_annotations(p = plot, x = data[[x_head]], y = data[[y_head]], text = highlight.labels, standoff = pointsize * scale, font = list(size = labelsize * scale), bgcolor = 'rgba(255, 255, 255, 0.5)')
-      }
+    if (!is.null(highlight.labels) && !is.null(highlight.data)) {
+      plot <- plotly::add_annotations(p = plot, x = highlight.data[[x_head]], y = highlight.data[[y_head]], text = highlight.labels, standoff = pointsize * scale, font = list(size = labelsize * scale), bgcolor = 'rgba(255, 255, 255, 0.5)')
+    }
+    if (!is.null(data.labels)) {
+      plot <- plotly::add_annotations(p = plot, x = data[[x_head]], y = data[[y_head]], text = data.labels, standoff = pointsize * scale, font = list(size = labelsize * scale), bgcolor = 'rgba(255, 255, 255, 0.5)')
     }
   }
 
diff --git a/R/scatterPlot.R b/R/scatterPlot.R
index 82dc67e..5a60367 100644
--- a/R/scatterPlot.R
+++ b/R/scatterPlot.R
@@ -116,17 +116,8 @@ scatterPlotUI <- function(id) {
 #' @param input Shiny's input object
 #' @param output Shiny's output object
 #' @param session Shiny's session object
-#' @param data data.table data visualized in plot (Supports reactive).
-#' @param types data.table: (Supports reactive)
-#'                        column1: colnames of data
-#'                        column2: corresponding column type
-#'                        column3: label (optional, used instead of id)
-#'                        column4: sub_label (optional, added to id/ label)
-#' @param x.names Character vector of column names(data column names) which will be available for x-axis. Can be reactive.
-#' @param y.names Character vector of column names(data column names) which will be available for y-axis. Can be reactive.
-#' @param z.names Character vector of column names(data column names) which will be available for z-axis. Can be reactive.
-#' @param features data.table of the features to mark (first column = id)
-#' @param markerReac reactive containing inputs of marker module.
+#' @param clarion A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)
+#' @param markerOutput Marker module output. See \code{\link[wilson]{marker}}.
 #' @param plot.method Choose to rather render a 'interactive' or 'static' plot. Defaults to 'static'.
 #' @param width Width of the plot in cm. Defaults to minimal size for readable labels and supports reactive.
 #' @param height Height of the plot in cm. Defaults to minimal size for readable labels and supports reactive.
@@ -135,30 +126,39 @@ scatterPlotUI <- function(id) {
 #'
 #' @return Returns reactive containing data used for plot.
 #'
-#' @details Make sure to have the same columnnames in data and features.
+#' @details As markerOutput provides a second dataset used for highlighting it is crucial for it to have the same columnnames as the dataset provided by clarion.
+#' @details Intersections between marker and clarion will be removed from clarion in favor of highlighting them.
 #'
 #' @export
-scatterPlot <- function(input, output, session, data, types, x.names = NULL, y.names = NULL, z.names = NULL, features = NULL, markerReac = NULL, plot.method = "static", width = "auto", height = "auto", ppi = 72, scale = 1) {
-  #handle reactive data
-  data.r <- shiny::reactive({
-    if(shiny::is.reactive(data)){
-      data <- data.table::copy(data())
-    }else{
-      data <- data.table::copy(data)
-    }
+scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, plot.method = "static", width = "auto", height = "auto", ppi = 72, scale = 1) {
+  # globals/ initialization #####
+  # clear plot
+  clearPlot <- shiny::reactiveVal(FALSE)
+  # disable downloadbutton on init
+  shinyjs::disable("download")
+  # set labelsize default for interactive
+  if (plot.method == "interactive") shiny::updateSliderInput(session = session, inputId = "labelsize", value = 10)
 
-    return(data)
-  })
-  #handle reactive features
-  features.r <- shiny::reactive({
-    if(shiny::is.reactive(features)){
-      features <- features()
-    }else{
-      features <- features
-    }
+  # input preparation #####
+  object <- shiny::reactive({
+    # support reactive
+    if (shiny::is.reactive(clarion)) {
+      if (!methods::is(clarion(), "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-    return(features)
+      obj <- clarion()$clone(deep = TRUE)
+    } else {
+      if (!methods::is(clarion, "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
+
+      obj <- clarion$clone(deep = TRUE)
+    }
   })
+  # create deep copy of marker data if existing
+  if (!is.null(markerOutput)) {
+    marker_object <- shiny::reactive({
+      markerOutput$clarion()$clone(deep = TRUE)
+    })
+  }
+
   # handle reactive sizes
   size <- shiny::reactive({
     width <- ifelse(shiny::is.reactive(width), width(), width)
@@ -166,13 +166,13 @@ scatterPlot <- function(input, output, session, data, types, x.names = NULL, y.n
     ppi <- ifelse(shiny::is.reactive(ppi), ppi(), ppi)
     scale <- ifelse(shiny::is.reactive(scale), scale(), scale)
 
-    if(!is.numeric(width) || width <= 0) {
+    if (!is.numeric(width) || width <= 0) {
       width <- "auto"
     }
-    if(!is.numeric(height) || height <= 0) {
+    if (!is.numeric(height) || height <= 0) {
       height <- "auto"
     }
-    if(!is.numeric(ppi) || ppi <= 0) {
+    if (!is.numeric(ppi) || ppi <= 0) {
       ppi <- 72
     }
 
@@ -182,152 +182,63 @@ scatterPlot <- function(input, output, session, data, types, x.names = NULL, y.n
          scale = scale)
   })
 
-  # available types for corresponding axis
-  types_x <- shiny::reactive({
-    if(shiny::is.reactive(types)) {
-      t <- types()
-    } else {
-      t <- types
-    }
-
-    if(shiny::is.reactive(x.names)) {
-      x <- x.names()
-    } else {
-      x <- x.names
-    }
-    if(is.null(x)) return(t)
-
-    t[key %in% x]
-  })
-
-  types_y <- shiny::reactive({
-    if(shiny::is.reactive(types)) {
-      t <- types()
-    } else {
-      t <- types
-    }
-
-    if(shiny::is.reactive(y.names)) {
-      y <- y.names()
-    } else {
-      y <- y.names
-    }
-    if(is.null(y)) return(t)
-
-    t[key %in% y]
-  })
-
-  types_z <- shiny::reactive({
-    if(shiny::is.reactive(types)) {
-      t <- types()
-    } else {
-      t <- types
-    }
-
-    if(shiny::is.reactive(z.names)) {
-      z <- z.names()
-    } else {
-      z <- z.names
-    }
-    if(is.null(z)) return(t)
-
-    t[key %in% z]
-  })
-
-  #Fetch the reactive guide for this module
-  guide <- scatterPlotGuide(session, !is.null(markerReac))
-  shiny::observeEvent(input$guide, {
-    rintrojs::introjs(session, options = list(steps = guide()))
-  })
-
-  data_x <- shiny::reactive(as.matrix(data.r()[, xaxis$selectedColumn(), with = FALSE]))
-  data_y <- shiny::reactive(as.matrix(data.r()[, yaxis$selectedColumn(), with = FALSE]))
-
-  # clear plot
-  clearPlot <- shiny::reactiveVal(FALSE)
-
-  #reset ui
-  shiny::observeEvent(input$reset, {
-    log_message("Scatterplot: reset", "INFO", token = session$token)
-
-    shinyjs::reset("density")
-    shinyjs::reset("line")
-    shinyjs::reset("pointsize")
-    shinyjs::reset("labelsize")
-    shinyjs::reset("force_cat")
-    xaxis <<- shiny::callModule(columnSelector, "xaxis", type.columns = types_x, columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_x$method()))
-    yaxis <<- shiny::callModule(columnSelector, "yaxis", type.columns = types_y, columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_y$method()))
-    zaxis <<- shiny::callModule(columnSelector, "zaxis", type.columns = types_z, columnTypeLabel = "Column type to choose from", multiple = FALSE, none = TRUE)
-    colorPicker <<- shiny::callModule(colorPicker2, "color", distribution = list("sequential", "diverging"), winsorize = winsorize)
-    transform_x <<- shiny::callModule(transformation, "transform_x", data = data_x)
-    transform_y <<- shiny::callModule(transformation, "transform_y", data = data_y)
-    limit_x <<- shiny::callModule(limit, "xaxis_limit", lower = shiny::reactive(result.data()$xlim[1]), upper = shiny::reactive(result.data()$xlim[2]))
-    limit_y <<- shiny::callModule(limit, "yaxis_limit", lower = shiny::reactive(result.data()$ylim[1]), upper = shiny::reactive(result.data()$ylim[2]))
-    clearPlot(TRUE)
-  })
-
-  winsorize <- shiny::reactive({
-    if(zaxis$selectedColumn() != "") {
-      equalize(result.data()$processed.data[, 4])
-    } else {
-      NULL
-    }
-  })
-
-  xaxis <- shiny::callModule(columnSelector, "xaxis", type.columns = types_x, columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_x$method()))
-  yaxis <- shiny::callModule(columnSelector, "yaxis", type.columns = types_y, columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_y$method()))
-  zaxis <- shiny::callModule(columnSelector, "zaxis", type.columns = types_z, columnTypeLabel = "Column type to choose from", labelLabel = "Color label", multiple = FALSE, none = TRUE)
-
-  colorPicker <- shiny::callModule(colorPicker2, "color", distribution = list("sequential", "diverging"), winsorize = winsorize)
-  transform_x <- shiny::callModule(transformation, "transform_x", data = data_x)
-  transform_y <- shiny::callModule(transformation, "transform_y", data = data_y)
+  # modules/ ui #####
+  xaxis <- shiny::callModule(columnSelector, "xaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_x$method()))
+  yaxis <- shiny::callModule(columnSelector, "yaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_y$method()))
+  zaxis <- shiny::callModule(columnSelector, "zaxis", type.columns = shiny::reactive(object()$metadata[, intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", labelLabel = "Color label", multiple = FALSE, none = TRUE)
+  colorPicker <- shiny::callModule(colorPicker2, "color", distribution = "all", winsorize = shiny::reactive(switch(shiny::isTruthy(zaxis$selectedColumn()) + 1, NULL, equalize(object()$data[, zaxis$selectedColumn(), with = FALSE]))))
+  transform_x <- shiny::callModule(transformation, "transform_x", data = shiny::reactive(as.matrix(object()$data[, xaxis$selectedColumn(), with = FALSE])))
+  transform_y <- shiny::callModule(transformation, "transform_y", data = shiny::reactive(as.matrix(object()$data[, yaxis$selectedColumn(), with = FALSE])))
+  # transform highlight data
+  if (!is.null(markerOutput)) {
+    # note: same id as transform_x/y so it depends on same ui
+    highlight_transform_x <- shiny::callModule(transformation, "transform_x", data = shiny::reactive(as.matrix(marker_object()$data[, xaxis$selectedColumn(), with = FALSE])))
+    highlight_transform_y <- shiny::callModule(transformation, "transform_y", data = shiny::reactive(as.matrix(marker_object()$data[, yaxis$selectedColumn(), with = FALSE])))
+  }
   limit_x <- shiny::callModule(limit, "xaxis_limit", lower = shiny::reactive(result.data()$xlim[1]), upper = shiny::reactive(result.data()$xlim[2]))
   limit_y <- shiny::callModule(limit, "yaxis_limit", lower = shiny::reactive(result.data()$ylim[1]), upper = shiny::reactive(result.data()$ylim[2]))
 
   # select container dependend on plot.method
-  if(plot.method == "static") {
+  if (plot.method == "static") {
     output$scatter <- shiny::renderUI({
       shinycssloaders::withSpinner(shiny::plotOutput(outputId = session$ns("static")), proxy.height = "800px")
     })
-  }else if(plot.method == "interactive") {
+  } else if (plot.method == "interactive") {
     output$scatter <- shiny::renderUI({
       shinycssloaders::withSpinner(plotly::plotlyOutput(outputId = session$ns("interactive")), proxy.height = "800px")
     })
   }
 
-  # show warning if there would more than 10 categories
-  shiny::observe({
-    shiny::req(!is.null(zaxis$selectedColumn()))
-
-    # something selected?
-    if(zaxis$selectedColumn() != "") {
-      # categories used?
-      if(input$force_cat || !is.numeric(data.r()[[zaxis$selectedColumn()]])) {
-        cat_num <- length(unique(data.r()[[zaxis$selectedColumn()]]))
-
-        if(cat_num > 10) {
-          shiny::showNotification(
-            id = session$ns("cat-limit"),
-            paste("Warning! There are", cat_num, "different categories selected. This can result in unexpected behavior. Recommended are 10 or less categories."),
-            duration = NULL,
-            type = "warning"
-          )
+  # functionality/ plotting #####
+  # reset ui
+  shiny::observeEvent(input$reset, {
+    log_message("Scatterplot: reset", "INFO", token = session$token)
 
-          shinyjs::runjs(paste0("$(document.getElementById('", paste0("shiny-notification-", session$ns("cat-limit")), "')).addClass('notification-position-center');"))
-        } else {
-          shiny::removeNotification(session$ns("cat-limit"))
-        }
-      } else {
-        shiny::removeNotification(session$ns("cat-limit"))
-      }
-    } else {
-      shiny::removeNotification(session$ns("cat-limit"))
+    shinyjs::reset("density")
+    shinyjs::reset("line")
+    shinyjs::reset("pointsize")
+    shinyjs::reset("labelsize")
+    shinyjs::reset("force_cat")
+    xaxis <<- shiny::callModule(columnSelector, "xaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_x$method()))
+    yaxis <<- shiny::callModule(columnSelector, "yaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_y$method()))
+    zaxis <<- shiny::callModule(columnSelector, "zaxis", type.columns = shiny::reactive(object()$metadata[, intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", multiple = FALSE, none = TRUE)
+    colorPicker <<- shiny::callModule(colorPicker2, "color", distribution = "all", winsorize = shiny::reactive(switch(shiny::isTruthy(zaxis$selectedColumn()) + 1, NULL, equalize(object()$data[, zaxis$selectedColumn(), with = FALSE]))))
+    transform_x <<- shiny::callModule(transformation, "transform_x", data = shiny::reactive(as.matrix(object()$data[, xaxis$selectedColumn(), with = FALSE])))
+    transform_y <<- shiny::callModule(transformation, "transform_y", data = shiny::reactive(as.matrix(object()$data[, yaxis$selectedColumn(), with = FALSE])))
+    # transform highlight data
+    if (!is.null(markerOutput)) {
+      # note: same id as transform_x/y so it depends on same ui
+      highlight_transform_x <<- shiny::callModule(transformation, "transform_x", data = shiny::reactive(as.matrix(marker_object()$data[, xaxis$selectedColumn(), with = FALSE])))
+      highlight_transform_y <<- shiny::callModule(transformation, "transform_y", data = shiny::reactive(as.matrix(marker_object()$data[, yaxis$selectedColumn(), with = FALSE])))
     }
+    limit_x <<- shiny::callModule(limit, "xaxis_limit", lower = shiny::reactive(result.data()$xlim[1]), upper = shiny::reactive(result.data()$xlim[2]))
+    limit_y <<- shiny::callModule(limit, "yaxis_limit", lower = shiny::reactive(result.data()$ylim[1]), upper = shiny::reactive(result.data()$ylim[2]))
+    clearPlot(TRUE)
   })
 
   # disable plot if mandatory x- or y-axis missing
   shiny::observe({
-    if(!shiny::isTruthy(xaxis$selectedColumn()) || !shiny::isTruthy(yaxis$selectedColumn())) {
+    if (!shiny::isTruthy(xaxis$selectedColumn()) || !shiny::isTruthy(yaxis$selectedColumn())) {
       shinyjs::disable("plot")
     } else {
       shinyjs::enable("plot")
@@ -335,111 +246,145 @@ scatterPlot <- function(input, output, session, data, types, x.names = NULL, y.n
   })
 
   transformed_data <- shiny::reactive({
-    #reassemble after transformation
-    if(zaxis$selectedColumn() != ""){
-      z <- data.table::data.table(data.r()[, zaxis$selectedColumn(), with = FALSE])
-      pre.data <- data.table::data.table(transform_x$data(), transform_y$data(), z)
-    }else{
-      pre.data <- data.table::data.table(transform_x$data(), transform_y$data())
+    # reassemble after transformation
+    # columns: unique_id, x, y(, z)
+    if (shiny::isTruthy(zaxis$selectedColumn())) {
+      z <- object()$data[, zaxis$selectedColumn(), with = FALSE]
+      pre.data <- data.table::data.table(object()$data[, object()$get_uniqueID(), with = FALSE], transform_x$data(), transform_y$data(), z)
+    } else {
+      pre.data <- data.table::data.table(object()$data[, object()$get_uniqueID(), with = FALSE], transform_x$data(), transform_y$data())
     }
 
-    #add rownames/ids
-    return(data.table::data.table(data.r()[, 1], pre.data))
+    return(pre.data)
   })
 
+  if (!is.null(markerOutput)) {
+    highlight_data <- shiny::reactive({
+      # return null on empty table
+      if (nrow(markerOutput$clarion()$data) == 0) return()
+      # reassemble after transformation
+      # columns: unique_id, x, y(, z)
+      if (shiny::isTruthy(zaxis$selectedColumn())) {
+        z <- object()$data[, zaxis$selectedColumn(), with = FALSE]
+        pre.data <- data.table::data.table(marker_object()$data[, marker_object()$get_uniqueID(), with = FALSE], highlight_transform_x$data(), highlight_transform_y$data(), z)
+      } else {
+        pre.data <- data.table::data.table(marker_object()$data[, marker_object()$get_uniqueID(), with = FALSE], highlight_transform_x$data(), highlight_transform_y$data())
+      }
+
+      return(pre.data)
+    })
+  }
+
   result.data <- shiny::eventReactive(input$plot, {
-    #new progress indicator
+    # new progress indicator
     progress <- shiny::Progress$new()
     on.exit(progress$close())
     progress$set(0, message = "Computing data")
 
     result <- list(
       processed.data = NULL,
+      data.label = NULL,
       highlight.color = NULL,
-      highlight.labels = NULL,
+      highlight.label = NULL,
       highlight.data = NULL,
       xlim = NULL,
       ylim = NULL
     )
 
-    #get selected data
+    # get selected data
     progress$set(0.3, detail = "transforming")
     processed.data <- transformed_data()
     progress$set(0.5, detail = "selecting")
 
-    #get axis limits
-    result$xlim <- c(min(processed.data[, 2], na.rm = TRUE), max(processed.data[, 2], na.rm = TRUE))
-    result$ylim <- c(min(processed.data[, 3], na.rm = TRUE), max(processed.data[, 3], na.rm = TRUE))
+    # no highlighting either disabled or N/A
+    if (is.null(markerOutput) || is.null(highlight_data()) || markerOutput$highlight() == "Disabled") {
+      # get axis limits
+      result$xlim <- c(min(processed.data[, 2], na.rm = TRUE), max(processed.data[, 2], na.rm = TRUE))
+      result$ylim <- c(min(processed.data[, 3], na.rm = TRUE), max(processed.data[, 3], na.rm = TRUE))
 
-    #get highlighted data
-    if(!is.null(markerReac) & !is.null(features.r())){
+      result$processed.data <- processed.data
+    } else {
+      # get highlight data
+      highlight.data <- highlight_data()
 
-      result$highlight.color <- markerReac()$color
-      if(markerReac()$highlight != "Disabled" & nrow(features.r()) > 0){
-        # restrict label to 100 or less
-        if(length(markerReac()$label) <= 100) {
-          result$highlight.labels <- markerReac()$label
-        } else {
+      # get axis limit including both datasets
+      result$xlim <- c(min(processed.data[, 2], highlight.data[, 2], na.rm = TRUE), max(processed.data[, 2], highlight.data[, 2], na.rm = TRUE))
+      result$ylim <- c(min(processed.data[, 3], highlight.data[, 3], na.rm = TRUE), max(processed.data[, 3], highlight.data[, 3], na.rm = TRUE))
+
+      # get colors
+      result$highlight.color <- markerOutput$color()
+
+      if (markerOutput$highlight() == "Highlight") {
+        # omit duplicates from processed.data
+        processed.data <- data.table::fsetdiff(x = processed.data, y = highlight.data)
+
+        # for everything duplicated = empty processed.data
+        if (nrow(processed.data) == 0) {
+          # notification that highlight color will be ignored
           shiny::showNotification(
-            id = session$ns("label-limit"),
-            paste("Warning! Label restricted to 100 or less labels. Currently selected:", length(markerReac()$label), "Please select fewer genes to label."),
+            id = session$ns("full_highlight"),
+            ui = "Ignoring highlight color as complete dataset is selected. Otherwise z-axis coloring would be lost.",
             duration = NULL,
             type = "warning"
           )
-          shinyjs::runjs(paste0("$(document.getElementById('", paste0("shiny-notification-", session$ns("label-limit")), "')).addClass('notification-position-center');"))
+          # show notification in center
+          shinyjs::runjs(paste0("$(document.getElementById('", paste0("shiny-notification-", session$ns("full_highlight")), "')).addClass('notification-position-center');"))
+
+          result$processed.data <- highlight.data
+        } else {
+          result$processed.data <- processed.data
+          result$highlight.data <- highlight.data
         }
-      }
 
-      if(markerReac()$highlight == "Highlight" & nrow(features.r()) > 0){
-        #overwrite columnnames because data.table makes unqiue names
-        result$highlight.data <- processed.data[features.r()[, names(features.r())[1], with = FALSE], on = names(features.r())[1]]
-        names(result$highlight.data) <- names(processed.data)
-        #sort out highlighted data
-        result$processed.data <- processed.data[!result$highlight.data, on = names(result$highlight.data)]
-      }else if(markerReac()$highlight == "Exclusive" & nrow(features.r()) > 0){
-        result$processed.data <- processed.data[features.r()[, names(features.r())[1], with = FALSE], on = names(features.r())[1]]
-      }else{
-        result$processed.data <- processed.data
+        # set label; ignore if more than 100
+        if (length(markerOutput$label()) <= 100) {
+          if (nrow(processed.data) == 0) {
+            result$data.label <- markerOutput$label()
+          } else {
+            result$highlight.label <- markerOutput$label()
+          }
+        }
+      } else if (markerOutput$highlight() == "Exclusive") {
+        result$processed.data <- highlight.data
+
+        # set label; ignore if more than 100
+        if (length(markerOutput$label()) <= 100) {
+          result$data.label <- markerOutput$label()
+        }
       }
-    }else{
-      result$processed.data <- processed.data
     }
 
     progress$set(1)
     return(result)
   })
 
-  #disable downloadbutton on init
-  shinyjs::disable("download")
-
   plot <- shiny::eventReactive(input$plot, {
     log_message("Scatterplot: computing plot...", "INFO", token = session$token)
 
-    #enable downloadbutton
+    # enable downloadbutton
     shinyjs::enable("download")
     clearPlot(FALSE)
 
-    #new progress indicator
+    # new progress indicator
     progress <- shiny::Progress$new()
     on.exit(progress$close())
     progress$set(0.2, message = "Computing plot")
 
-    colors <- colorPicker()$palette
-
-    if(!is.null(limit_x())) {
-      xlimit <- unlist(unname(limit_x()))
+    if (!is.null(limit_x())) {
+      xlimit <- unlist(limit_x())
     } else {
       xlimit <- result.data()$xlim
     }
-    if(!is.null(limit_y())) {
-      ylimit <- unlist(unname(limit_y()))
+    if (!is.null(limit_y())) {
+      ylimit <- unlist(limit_y())
     } else {
       ylimit <- result.data()$ylim
     }
 
     plot <- create_scatterplot(
       data = result.data()$processed.data,
-      colors = colors,
+      data.labels = result.data()$data.label,
+      color = colorPicker()$palette,
       x_label = xaxis$label(),
       y_label = yaxis$label(),
       z_label = zaxis$label(),
@@ -450,7 +395,7 @@ scatterPlot <- function(input, output, session, data, types, x.names = NULL, y.n
       line = input$line,
       highlight.data = result.data()$highlight.data,
       highlight.color = result.data()$highlight.color,
-      highlight.labels = result.data()$highlight.labels,
+      highlight.labels = result.data()$highlight.label,
       xlim = xlimit,
       ylim = ylimit,
       colorbar.limits = colorPicker()$winsorize,
@@ -459,7 +404,7 @@ scatterPlot <- function(input, output, session, data, types, x.names = NULL, y.n
       height = size()$height,
       ppi = size()$ppi,
       scale = size()$scale,
-      categorized = if(input$force_cat || ncol(result.data()$processed.data) >= 4 && !is.numeric(result.data()$processed.data[[4]])) TRUE else FALSE
+      categorized = if (input$force_cat || ncol(result.data()$processed.data) >= 4 && !is.numeric(result.data()$processed.data[[4]])) TRUE else FALSE
     )
 
     progress$set(1)
@@ -467,25 +412,13 @@ scatterPlot <- function(input, output, session, data, types, x.names = NULL, y.n
     return(plot)
   })
 
-  # warning if plot size exceeds limits
-  shiny::observe({
-    if(plot()$exceed_size) {
-      shiny::showNotification(
-        ui = "Width and/ or height exceed limit. Using 500 cm instead.",
-        id = "limit",
-        type = "warning"
-      )
-    } else {
-      shiny::removeNotification("limit")
-    }
-  })
-
-  if(plot.method == "static") {
+  # render plot #####
+  if (plot.method == "static") {
     output$static <- shiny::renderPlot(
       width = shiny::reactive(plot()$width * (plot()$ppi / 2.54)),
       height = shiny::reactive(plot()$height * (plot()$ppi / 2.54)),
       {
-        if(clearPlot()) {
+        if (clearPlot()) {
           return()
         } else {
           log_message("Scatterplot: render plot static", "INFO", token = session$token)
@@ -494,14 +427,14 @@ scatterPlot <- function(input, output, session, data, types, x.names = NULL, y.n
         }
       }
     )
-  } else if(plot.method == "interactive") {
+  } else if (plot.method == "interactive") {
     output$interactive <- plotly::renderPlotly({
-      if(clearPlot()) {
+      if (clearPlot()) {
         return()
       } else {
         log_message("Scatterplot: render plot interactive", "INFO", token = session$token)
 
-        #new progress indicator
+        # new progress indicator
         progress <- shiny::Progress$new()
         on.exit(progress$close())
         progress$set(0.2, message = "Render plot")
@@ -514,6 +447,7 @@ scatterPlot <- function(input, output, session, data, types, x.names = NULL, y.n
     })
   }
 
+  # download #####
   output$download <- shiny::downloadHandler(filename = "scatterPlot.zip",
     content = function(file) {
       log_message("Scatterplot: download", "INFO", token = session$token)
@@ -521,7 +455,6 @@ scatterPlot <- function(input, output, session, data, types, x.names = NULL, y.n
     }
   )
 
-
   user_input <- shiny::reactive({
     # format axis
     xaxis <- lapply(xaxis, function(x) { x() })
@@ -547,14 +480,84 @@ scatterPlot <- function(input, output, session, data, types, x.names = NULL, y.n
 
     # format marker
     marker <- NULL
-    if(!is.null(markerReac)) {
-      marker <- markerReac()
+    if (!is.null(markerOutput)) {
+      marker <- list(
+        highlight = markerOutput$highlight(),
+        color = markerOutput$color(),
+        labelColumn = markerOutput$labelColumn(),
+        label = markerOutput$label()
+      )
     }
 
-    #merge all
+    # merge all
     all <- list(axis = axis, appearance = appearance, options = options, marker = marker)
   })
 
+  # notifications #####
+  # show warning if there would be more than 10 categories
+  shiny::observe({
+    # something selected?
+    if (shiny::isTruthy(zaxis$selectedColumn())) {
+      # categories used?
+      if (input$force_cat || !is.numeric(object()$data[[zaxis$selectedColumn()]])) {
+        cat_num <- length(unique(object()$data[[zaxis$selectedColumn()]]))
+
+        if (cat_num > 10) {
+          shiny::showNotification(
+            id = session$ns("cat-limit"),
+            paste("Warning! There are", cat_num, "different categories selected. This can result in unexpected behavior. Recommended are 10 or less categories."),
+            duration = NULL,
+            type = "warning"
+          )
+
+          shinyjs::runjs(paste0("$(document.getElementById('", paste0("shiny-notification-", session$ns("cat-limit")), "')).addClass('notification-position-center');"))
+        } else {
+          shiny::removeNotification(session$ns("cat-limit"))
+        }
+      } else {
+        shiny::removeNotification(session$ns("cat-limit"))
+      }
+    } else {
+      shiny::removeNotification(session$ns("cat-limit"))
+    }
+  })
+
+  # warning if plot size exceeds limits
+  shiny::observe({
+    if (plot()$exceed_size) {
+      shiny::showNotification(
+        ui = "Width and/ or height exceed limit. Using 500 cm instead.",
+        id = session$ns("limit"),
+        type = "warning"
+      )
+    } else {
+      shiny::removeNotification(session$ns("limit"))
+    }
+  })
+
+  # label restriction warning
+  if (!is.null(markerOutput)) {
+    shiny::observe({
+      if (markerOutput$highlight() != "Disabled" && length(markerOutput$label()) > 100) {
+        shiny::showNotification(
+          id = session$ns("label-limit"),
+          paste("Warning! Label restricted to 100 or less labels. Currently selected:", length(markerOutput$label()), "Please select fewer genes to label or else they will be ignored."),
+          duration = NULL,
+          type = "warning"
+        )
+        shinyjs::runjs(paste0("$(document.getElementById('", paste0("shiny-notification-", session$ns("label-limit")), "')).addClass('notification-position-center');"))
+      } else {
+        shiny::removeNotification(session$ns("label-limit"))
+      }
+    })
+  }
+
+  # Fetch the reactive guide for this module
+  guide <- scatterPlotGuide(session, !is.null(markerOutput))
+  shiny::observeEvent(input$guide, {
+    rintrojs::introjs(session, options = list(steps = guide()))
+  })
+
   return(shiny::reactive({unique(data.table::rbindlist(list(result.data()$processed.data, result.data()$highlight.data)))}))
 }
 
@@ -598,8 +601,8 @@ scatterPlotGuide <- function(session, marker = FALSE) {
       As a final step, a click on the 'Plot' button will render the plot, while a click on the 'Reset' button will reset the parameters to default."
   )
 
-  #add marker text to guide
-  if(marker){
+  # add marker text to guide
+  if (marker) {
     steps <- append(steps,
                     list("guide_marker" = "<h4>Highlighting</h4>
                           If a set of features is selected, it is possible to either 'Highlight' those data points in the selected color or to show them 'Exclusively', omitting all other data points.<br/>
diff --git a/exec/scatterPlot_example.R b/exec/scatterPlot_example.R
index 292c753..7a16840 100644
--- a/exec/scatterPlot_example.R
+++ b/exec/scatterPlot_example.R
@@ -10,12 +10,14 @@ source("../R/marker.R")
 source("../R/limit.R")
 source("../R/label.R")
 source("../R/global.R")
+source("../R/clarion.R")
 
 ####Test Data
-data <- data.table::data.table(id = rownames(mtcars), mtcars)
+data <- data.table::as.data.table(mtcars, keep.rowname = "id")
 # create metadata
-metadata <- data.table::data.table(names(data), level = c("annotation", rep("performance", 7), rep("design", 4)))
+metadata <- data.table::data.table(names(data), level = c("feature", rep("sample", 7), rep("condition", 4)))
 names(metadata)[1] <- "key"
+clarion <- Clarion$new(data = data, metadata = metadata)
 ####
 
 ui <- dashboardPage(header = dashboardHeader(),
@@ -33,9 +35,11 @@ ui <- dashboardPage(header = dashboardHeader(),
 )
 
 server <- function(input, output) {
-  marker <- callModule(marker, "marker", data)
-  # highlight all manual cars
-  plot <- callModule(scatterPlot, "id", data = data, types = metadata, x.names = metadata[level != "annotation"][["key"]], y.names = metadata[level != "annotation"][["key"]], features = data[am == 1], markerReac = marker, plot.method = "interactive", width = reactive(input$width), height = reactive(input$height), scale = reactive(input$scale))
+  # highlight first 10 cars
+  marked <- Clarion$new(metadata = metadata, data = data[1:10])
+  marker <- callModule(marker, "marker", clarion = marked)
+
+  plot <- callModule(scatterPlot, "id", clarion = clarion, markerOutput = marker, plot.method = "interactive", width = reactive(input$width), height = reactive(input$height), scale = reactive(input$scale))
 
   observe({
     print(plot())
diff --git a/man/create_scatterplot.Rd b/man/create_scatterplot.Rd
index 1eb26de..776ecb7 100644
--- a/man/create_scatterplot.Rd
+++ b/man/create_scatterplot.Rd
@@ -4,25 +4,28 @@
 \alias{create_scatterplot}
 \title{Method for scatter plot creation}
 \usage{
-create_scatterplot(data, transparency = 1, pointsize = 1, labelsize = 3,
-  colors = NULL, x_label = "", y_label = "", z_label = "",
-  density = T, line = T, categorized = F, highlight.data = NULL,
-  highlight.labels = NULL, highlight.color = "#FF0000", xlim = NULL,
-  ylim = NULL, colorbar.limits = NULL, width = "auto", height = "auto",
-  ppi = 72, plot.method = "static", scale = 1)
+create_scatterplot(data, data.labels = NULL, transparency = 1,
+  pointsize = 1, labelsize = 3, color = NULL, x_label = "",
+  y_label = "", z_label = "", density = T, line = T, categorized = F,
+  highlight.data = NULL, highlight.labels = NULL,
+  highlight.color = "#FF0000", xlim = NULL, ylim = NULL,
+  colorbar.limits = NULL, width = "auto", height = "auto", ppi = 72,
+  plot.method = "static", scale = 1)
 }
 \arguments{
 \item{data}{data.table containing plot data
 column 1: id
 column 2, 3(, 4): x, y(, z)}
 
+\item{data.labels}{Vector of labels used for data. Length has to be equal to nrow(data).}
+
 \item{transparency}{Set point transparency. See \code{\link[ggplot2]{geom_point}}.}
 
 \item{pointsize}{Set point size. See \code{\link[ggplot2]{geom_point}}.}
 
 \item{labelsize}{Set label size. See \code{\link[ggplot2]{geom_text}}.}
 
-\item{colors}{Vector of colors used for color palette}
+\item{color}{Vector of colors used for color palette.}
 
 \item{x_label}{Label x-Axis}
 
@@ -36,9 +39,9 @@ column 2, 3(, 4): x, y(, z)}
 
 \item{categorized}{Z-Axis (if exists) as categories.}
 
-\item{highlight.data}{data.table containing data to highlight.}
+\item{highlight.data}{data.table containing data to highlight. Same structure as data.}
 
-\item{highlight.labels}{Vector of labels used for highlighted data.}
+\item{highlight.labels}{Vector of labels used for highlighted data. Length has to be equal to nrow(data).}
 
 \item{highlight.color}{String with hexadecimal color-code.}
 
diff --git a/man/scatterPlot.Rd b/man/scatterPlot.Rd
index 7d7489b..9cb7168 100644
--- a/man/scatterPlot.Rd
+++ b/man/scatterPlot.Rd
@@ -4,8 +4,7 @@
 \alias{scatterPlot}
 \title{scatterPlot module server logic}
 \usage{
-scatterPlot(input, output, session, data, types, x.names = NULL,
-  y.names = NULL, z.names = NULL, features = NULL, markerReac = NULL,
+scatterPlot(input, output, session, clarion, markerOutput = NULL,
   plot.method = "static", width = "auto", height = "auto", ppi = 72,
   scale = 1)
 }
@@ -16,23 +15,9 @@ scatterPlot(input, output, session, data, types, x.names = NULL,
 
 \item{session}{Shiny's session object}
 
-\item{data}{data.table data visualized in plot (Supports reactive).}
+\item{clarion}{A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)}
 
-\item{types}{data.table: (Supports reactive)
-column1: colnames of data
-column2: corresponding column type
-column3: label (optional, used instead of id)
-column4: sub_label (optional, added to id/ label)}
-
-\item{x.names}{Character vector of column names(data column names) which will be available for x-axis. Can be reactive.}
-
-\item{y.names}{Character vector of column names(data column names) which will be available for y-axis. Can be reactive.}
-
-\item{z.names}{Character vector of column names(data column names) which will be available for z-axis. Can be reactive.}
-
-\item{features}{data.table of the features to mark (first column = id)}
-
-\item{markerReac}{reactive containing inputs of marker module.}
+\item{markerOutput}{Marker module output. See \code{\link[wilson]{marker}}.}
 
 \item{plot.method}{Choose to rather render a 'interactive' or 'static' plot. Defaults to 'static'.}
 
@@ -51,5 +36,7 @@ Returns reactive containing data used for plot.
 scatterPlot module server logic
 }
 \details{
-Make sure to have the same columnnames in data and features.
+As markerOutput provides a second dataset used for highlighting it is crucial for it to have the same columnnames as the dataset provided by clarion.
+
+Intersections between marker and clarion will be removed from clarion in favor of highlighting them.
 }

From d4b5240bc1081279c2c6762168436066495c18ed Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 16 May 2018 12:25:07 +0200
Subject: [PATCH 20/75] clarion: also coerce name to character

---
 R/clarion.R | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/R/clarion.R b/R/clarion.R
index 05989a7..61922b8 100644
--- a/R/clarion.R
+++ b/R/clarion.R
@@ -70,8 +70,13 @@ Clarion <- R6::R6Class("Clarion",
                            self$metadata <- metadata
                            self$data <- data
 
-                           # coerce unique_id to character
-                           self$data[, (self$get_uniqueID()) := sapply(.SD, as.character), .SDcols = self$get_uniqueID()]
+                           # coerce unique_id and name to character
+                           if (self$get_uniqueID() == self$get_name()) {
+                             cols <- self$get_uniqueID()
+                           } else {
+                             cols <- c(self$get_uniqueID(), self$get_name())
+                           }
+                           self$data[, (cols) := lapply(.SD, as.character), .SDcols = cols]
 
                            if (validate) self$validate()
                          }

From 80deb83045ef7dcc5b0f3252bbd7e58be9f5a8a7 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 17 May 2018 10:33:35 +0200
Subject: [PATCH 21/75] scatterplot: add names to hovertext

---
 R/function.R              | 61 +++++++++++++++++++++++++--------------
 R/scatterPlot.R           | 31 +++++++++++++++++++-
 man/create_scatterplot.Rd | 20 ++++++++-----
 3 files changed, 82 insertions(+), 30 deletions(-)

diff --git a/R/function.R b/R/function.R
index 762bb3c..7fb0939 100644
--- a/R/function.R
+++ b/R/function.R
@@ -4,6 +4,7 @@
 #'             column 1: id
 #'             column 2, 3(, 4): x, y(, z)
 #' @param data.labels Vector of labels used for data. Length has to be equal to nrow(data).
+#' @param data.hovertext Character vector with additional hovertext. Length has to be equal to nrow(data).
 #' @param transparency Set point transparency. See \code{\link[ggplot2]{geom_point}}.
 #' @param pointsize Set point size. See \code{\link[ggplot2]{geom_point}}.
 #' @param labelsize Set label size. See \code{\link[ggplot2]{geom_text}}.
@@ -15,7 +16,8 @@
 #' @param line Boolean value, add reference line.
 #' @param categorized Z-Axis (if exists) as categories.
 #' @param highlight.data data.table containing data to highlight. Same structure as data.
-#' @param highlight.labels Vector of labels used for highlighted data. Length has to be equal to nrow(data).
+#' @param highlight.labels Vector of labels used for highlighted data. Length has to be equal to nrow(highlight.data).
+#' @param highlight.hovertext Character vector with additional hovertext. Length has to be equal to nrow(highlight.data).
 #' @param highlight.color String with hexadecimal color-code.
 #' @param xlim Numeric vector of two setting min and max limit of x-axis. See \code{\link[ggplot2]{lims}}.
 #' @param ylim Numeric vector of two setting min and max limit of y-axis. See \code{\link[ggplot2]{lims}}.
@@ -31,7 +33,7 @@
 #' @import data.table
 #'
 #' @return Returns list(plot = ggplotly/ ggplot, width, height, ppi, exceed_size).
-create_scatterplot <- function(data, data.labels = NULL, transparency = 1, pointsize = 1, labelsize = 3, color = NULL, x_label = "", y_label = "", z_label = "", density = T, line = T, categorized = F, highlight.data = NULL, highlight.labels = NULL, highlight.color = "#FF0000", xlim = NULL, ylim = NULL, colorbar.limits = NULL, width = "auto", height = "auto", ppi = 72, plot.method = "static", scale = 1){
+create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL, transparency = 1, pointsize = 1, labelsize = 3, color = NULL, x_label = "", y_label = "", z_label = "", density = T, line = T, categorized = F, highlight.data = NULL, highlight.labels = NULL, highlight.hovertext = NULL, highlight.color = "#FF0000", xlim = NULL, ylim = NULL, colorbar.limits = NULL, width = "auto", height = "auto", ppi = 72, plot.method = "static", scale = 1){
   ########## prepare data ##########
   # set labelnames if needed
   x_label <- ifelse(nchar(x_label), x_label, names(data)[2])
@@ -59,10 +61,12 @@ create_scatterplot <- function(data, data.labels = NULL, transparency = 1, point
     highlight.data <- highlight.data[rows.to.keep.high]
   }
 
-  # delete labels accordingly
+  # delete labels & hovertext accordingly
   data.labels <- data.labels[rows.to.keep.data]
+  data.hovertext <- data.hovertext[rows.to.keep.data]
   if (!is.null(highlight.data)) {
     highlight.labels <- highlight.labels[rows.to.keep.high]
+    highlight.hovertext <- highlight.hovertext[rows.to.keep.high]
   }
 
   ########## assemble plot ##########
@@ -137,36 +141,51 @@ create_scatterplot <- function(data, data.labels = NULL, transparency = 1, point
   # interactive points with hovertexts
   if (plot.method == "interactive") {
     # set hovertext
+    # list of arguments for paste0
+    args <- list(
+      "</br>", data[[1]],
+      "</br>", x_label, ": ", data[[x_head]],
+      "</br>", y_label, ": ", data[[y_head]]
+    )
+
+    # append z-axis
     if (ncol(data) >= 4) {
-      hovertext <- paste0("</br>", data[[1]],
-                          "</br>", x_label, ": ", data[[x_head]],
-                          "</br>", y_label, ": ", data[[y_head]],
-                          "</br>", z_label, ": ", data[[z_head]])
-    } else {
-      hovertext <- paste0("</br>", data[[1]],
-                          "</br>", x_label, ": ", data[[x_head]],
-                          "</br>", y_label, ": ", data[[y_head]])
+      args <- append(args, list("</br>", z_label, ": ", data[[z_head]]))
     }
+    # append additional hovertext
+    if (!is.null(data.hovertext)) {
+      args <- append(args, list("</br>", data.hovertext), after = 2)
+    }
+
+    # eval arguments with paste0
+    hovertext <- do.call(paste0, args)
 
     # set points
-    # color if no z-axis
     plot <- plot + ggplot2::geom_point(size = pointsize * scale, alpha = transparency, ggplot2::aes(text = hovertext))
 
     if (!is.null(highlight.data)) {
       # set highlighted hovertext
+      # list of arguments for paste0
+      highlight.args <- list(
+        "</br>", highlight.data[[1]],
+        "</br>", x_label, ": ", highlight.data[[x_head]],
+        "</br>", y_label, ": ", highlight.data[[y_head]]
+      )
+
+      # append z-axis
       if (ncol(data) >= 4) {
-        hovertext.high <- paste0("</br>", highlight.data[[1]],
-                                 "</br>", x_label, ": ", highlight.data[[x_head]],
-                                 "</br>", y_label, ": ", highlight.data[[y_head]],
-                                 "</br>", z_label, ": ", highlight.data[[z_head]])
-      } else {
-        hovertext.high <- paste0("</br>", highlight.data[[1]],
-                                 "</br>", x_label, ": ", highlight.data[[x_head]],
-                                 "</br>", y_label, ": ", highlight.data[[y_head]])
+        highlight.args <- append(highlight.args, list("</br>", z_label, ": ", highlight.data[[z_head]]))
       }
+      # append additional hovertext
+      if (!is.null(highlight.hovertext)) {
+        highlight.args <- append(highlight.args, list("</br>", highlight.hovertext), after = 2)
+      }
+
+      # eval arguments with paste0
+      highlight.hovertext <- do.call(paste0, highlight.args)
 
       # set highlighted points
-      plot <- plot + ggplot2::geom_point(size = pointsize * scale, alpha = transparency, inherit.aes = TRUE, data = highlight.data, color = highlight.color, show.legend = FALSE, ggplot2::aes(text = hovertext.high))
+      plot <- plot + ggplot2::geom_point(size = pointsize * scale, alpha = transparency, inherit.aes = TRUE, data = highlight.data, color = highlight.color, show.legend = FALSE, ggplot2::aes(text = highlight.hovertext))
     }
   # static points without hovertexts
   } else if (plot.method == "static") {
diff --git a/R/scatterPlot.R b/R/scatterPlot.R
index 5a60367..2ae8830 100644
--- a/R/scatterPlot.R
+++ b/R/scatterPlot.R
@@ -265,7 +265,7 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
       # reassemble after transformation
       # columns: unique_id, x, y(, z)
       if (shiny::isTruthy(zaxis$selectedColumn())) {
-        z <- object()$data[, zaxis$selectedColumn(), with = FALSE]
+        z <- marker_object()$data[, zaxis$selectedColumn(), with = FALSE]
         pre.data <- data.table::data.table(marker_object()$data[, marker_object()$get_uniqueID(), with = FALSE], highlight_transform_x$data(), highlight_transform_y$data(), z)
       } else {
         pre.data <- data.table::data.table(marker_object()$data[, marker_object()$get_uniqueID(), with = FALSE], highlight_transform_x$data(), highlight_transform_y$data())
@@ -284,8 +284,10 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
     result <- list(
       processed.data = NULL,
       data.label = NULL,
+      data.hovertext = NULL,
       highlight.color = NULL,
       highlight.label = NULL,
+      highlight.hovertext = NULL,
       highlight.data = NULL,
       xlim = NULL,
       ylim = NULL
@@ -302,6 +304,11 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
       result$xlim <- c(min(processed.data[, 2], na.rm = TRUE), max(processed.data[, 2], na.rm = TRUE))
       result$ylim <- c(min(processed.data[, 3], na.rm = TRUE), max(processed.data[, 3], na.rm = TRUE))
 
+      # add name to hovertext
+      if (plot.method == "interactive" && object()$get_name() != object()$get_uniqueID()) {
+        result$data.hovertext <- object()$data[[object()$get_name()]]
+      }
+
       result$processed.data <- processed.data
     } else {
       # get highlight data
@@ -330,8 +337,23 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
           # show notification in center
           shinyjs::runjs(paste0("$(document.getElementById('", paste0("shiny-notification-", session$ns("full_highlight")), "')).addClass('notification-position-center');"))
 
+          # add name to hovertext
+          if (plot.method == "interactive" && marker_object()$get_name() != marker_object()$get_uniqueID()) {
+            result$data.hovertext <- marker_object()$data[[marker_object()$get_name()]]
+          }
+
           result$processed.data <- highlight.data
         } else {
+          # add name to hovertext
+          if (plot.method == "interactive" && object()$get_name() != object()$get_uniqueID()) {
+            # only keep selected rows
+            result$data.hovertext <- object()$data[processed.data, on = object()$get_uniqueID()][[object()$get_name()]]
+          }
+          # add name to hovertext
+          if (plot.method == "interactive" && marker_object()$get_name() != marker_object()$get_uniqueID()) {
+            result$highlight.hovertext <- marker_object()$data[[marker_object()$get_name()]]
+          }
+
           result$processed.data <- processed.data
           result$highlight.data <- highlight.data
         }
@@ -345,6 +367,11 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
           }
         }
       } else if (markerOutput$highlight() == "Exclusive") {
+        # add name to hovertext
+        if (plot.method == "interactive" && marker_object()$get_name() != marker_object()$get_uniqueID()) {
+          result$data.hovertext <- marker_object()$data[[marker_object()$get_name()]]
+        }
+
         result$processed.data <- highlight.data
 
         # set label; ignore if more than 100
@@ -384,6 +411,7 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
     plot <- create_scatterplot(
       data = result.data()$processed.data,
       data.labels = result.data()$data.label,
+      data.hovertext <- result.data()$data.hovertext,
       color = colorPicker()$palette,
       x_label = xaxis$label(),
       y_label = yaxis$label(),
@@ -396,6 +424,7 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
       highlight.data = result.data()$highlight.data,
       highlight.color = result.data()$highlight.color,
       highlight.labels = result.data()$highlight.label,
+      highlight.hovertext = result.data()$highlight.hovertext,
       xlim = xlimit,
       ylim = ylimit,
       colorbar.limits = colorPicker()$winsorize,
diff --git a/man/create_scatterplot.Rd b/man/create_scatterplot.Rd
index 776ecb7..1e60d4b 100644
--- a/man/create_scatterplot.Rd
+++ b/man/create_scatterplot.Rd
@@ -4,13 +4,13 @@
 \alias{create_scatterplot}
 \title{Method for scatter plot creation}
 \usage{
-create_scatterplot(data, data.labels = NULL, transparency = 1,
-  pointsize = 1, labelsize = 3, color = NULL, x_label = "",
-  y_label = "", z_label = "", density = T, line = T, categorized = F,
-  highlight.data = NULL, highlight.labels = NULL,
-  highlight.color = "#FF0000", xlim = NULL, ylim = NULL,
-  colorbar.limits = NULL, width = "auto", height = "auto", ppi = 72,
-  plot.method = "static", scale = 1)
+create_scatterplot(data, data.labels = NULL, data.hovertext = NULL,
+  transparency = 1, pointsize = 1, labelsize = 3, color = NULL,
+  x_label = "", y_label = "", z_label = "", density = T, line = T,
+  categorized = F, highlight.data = NULL, highlight.labels = NULL,
+  highlight.hovertext = NULL, highlight.color = "#FF0000", xlim = NULL,
+  ylim = NULL, colorbar.limits = NULL, width = "auto", height = "auto",
+  ppi = 72, plot.method = "static", scale = 1)
 }
 \arguments{
 \item{data}{data.table containing plot data
@@ -19,6 +19,8 @@ column 2, 3(, 4): x, y(, z)}
 
 \item{data.labels}{Vector of labels used for data. Length has to be equal to nrow(data).}
 
+\item{data.hovertext}{Character vector with additional hovertext. Length has to be equal to nrow(data).}
+
 \item{transparency}{Set point transparency. See \code{\link[ggplot2]{geom_point}}.}
 
 \item{pointsize}{Set point size. See \code{\link[ggplot2]{geom_point}}.}
@@ -41,7 +43,9 @@ column 2, 3(, 4): x, y(, z)}
 
 \item{highlight.data}{data.table containing data to highlight. Same structure as data.}
 
-\item{highlight.labels}{Vector of labels used for highlighted data. Length has to be equal to nrow(data).}
+\item{highlight.labels}{Vector of labels used for highlighted data. Length has to be equal to nrow(highlight.data).}
+
+\item{highlight.hovertext}{Character vector with additional hovertext. Length has to be equal to nrow(highlight.data).}
 
 \item{highlight.color}{String with hexadecimal color-code.}
 

From 95eb6eb003a957bc95585dab2c11f56de582621d Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Tue, 22 May 2018 13:08:27 +0200
Subject: [PATCH 22/75] pca: color and shape based grouping enabled

---
 R/function.R       | 114 +++++++++++++++++++++++++++++++++------------
 R/pca.R            |  87 ++++++++++++++++++++++------------
 exec/pca_example.R |   5 +-
 man/create_pca.Rd  |  21 +++++++--
 4 files changed, 162 insertions(+), 65 deletions(-)

diff --git a/R/function.R b/R/function.R
index 7fb0939..6951343 100644
--- a/R/function.R
+++ b/R/function.R
@@ -294,6 +294,12 @@ create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL,
 #' Method for pca creation.
 #'
 #' @param data data.table from which the plot is created (First column will be handled as rownames if not numeric).
+#' @param color.group Vector of groups according to samples (= column names).
+#' @param color.title Title of the color legend.
+#' @param palette Vector of colors used for color palette.
+#' @param shape.group Vector of groups according to samples (= column names).
+#' @param shape.title Title of the shape legend.
+#' @param shapes Vector of shapes see \code{\link[graphics]{points}}. Will recycle/ cut off shapes if needed. Default = c(15:25)
 #' @param dimensionA Number of dimension displayed on X-Axis.
 #' @param dimensionB Number of dimension displayed on Y-Axis.
 #' @param dimensions Number of dimesions to create.
@@ -313,76 +319,124 @@ create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL,
 #' @import data.table
 #'
 #' @return A named list(plot = ggplot object, data = pca.data, width = width of plot (cm), height = height of plot (cm), ppi = pixel per inch, exceed_size = Boolean whether width/ height exceeded max).
-create_pca <- function(data, dimensionA = 1, dimensionB = 2, dimensions = 6, on.columns = TRUE, labels = FALSE, custom.labels = NULL, pointsize = 2, labelsize = 3, width = 28, height = 28, ppi = 72, scale = 1) {
+create_pca <- function(data, color.group = NULL, color.title = NULL, palette = NULL, shape.group = NULL, shape.title = NULL, shapes = c(15:25), dimensionA = 1, dimensionB = 2, dimensions = 6, on.columns = TRUE, labels = FALSE, custom.labels = NULL, pointsize = 2, labelsize = 3, width = 28, height = 28, ppi = 72, scale = 1) {
   requireNamespace("FactoMineR", quietly = TRUE)
   requireNamespace("factoextra", quietly = TRUE)
 
   # prepare data ------------------------------------------------------------
   # set custom labels
-  if(!is.null(custom.labels)) {
-    if(!is.numeric(data[[1]])) {
+  if (!is.null(custom.labels)) {
+    if (!is.numeric(data[[1]])) {
       colnames(data)[-1] <- custom.labels
     } else {
       colnames(data) <- custom.labels
     }
   }
 
-  #remove rows with NA
+  # remove rows with NA
   data <- stats::na.omit(data)
 
-  #check for rownames
-  if(!is.numeric(data[[1]])){
+  # check for rownames
+  if (!is.numeric(data[[1]])) {
     rownames <- data[[1]]
     data[, 1 := NULL]
-  }else{
+  } else {
     rownames <- NULL
   }
 
-  #transpose
-  if(on.columns){
+  # transpose
+  if (on.columns) {
     data_t <- t(data)
-    if(!is.null(rownames)){
+    if (!is.null(rownames)) {
       colnames(data_t) <- rownames
     }
-  }else{
+  } else {
     data_t <- as.matrix(data)
-    if(!is.null(rownames)){
+    if (!is.null(rownames)) {
       rownames(data_t) <- rownames
     }
   }
 
-  #check if PCA possible
-  if(ncol(data_t) < 3){
+  # check if PCA possible
+  if (ncol(data_t) < 3) {
     stop(paste("PCA requires at least 3 elements. Found:", ncol(data_t)))
   }
 
-  #remove constant rows (=genes with the same value for all samples)
+  # remove constant rows (= genes with the same value for all samples)
   data_t <- data_t[, apply(data_t, 2, function(x) min(x, na.rm = TRUE) != max(x, na.rm = TRUE))]
 
   pca <- FactoMineR::PCA(data_t, scale.unit = TRUE, ncp = dimensions, graph = FALSE)
 
   # plot --------------------------------------------------------------------
-  theme1 <- ggplot2::theme (								#no gray background or helper lines
+  theme1 <- ggplot2::theme(								# no gray background or helper lines
     plot.background = ggplot2::element_blank(),
     panel.grid.major = ggplot2::element_blank(),
     panel.grid.minor = ggplot2::element_blank(),
     panel.border = ggplot2::element_blank(),
     panel.background = ggplot2::element_blank(),
-    axis.line.x = ggplot2::element_line(size=.3),
-    axis.line.y = ggplot2::element_line(size=.3),
-    axis.title.x = ggplot2::element_text(color="black", size = 11 * scale),
-    axis.title.y = ggplot2::element_text(color="black", size = 11 * scale),
-    #plot.title = element_text(color="black", size=12),
+    axis.line.x = ggplot2::element_line(size = .3),
+    axis.line.y = ggplot2::element_line(size = .3),
+    axis.title.x = ggplot2::element_text(color = "black", size = 11 * scale),
+    axis.title.y = ggplot2::element_text(color = "black", size = 11 * scale),
+    # plot.title = element_text(color = "black", size = 12),
     plot.title = ggplot2::element_blank(),
-    legend.title = ggplot2::element_blank(),
-    text = ggplot2::element_text(size = 12 * scale)						#size for all (legend?) labels
-    #legend.key = element_rect(fill="white")
+    legend.title = ggplot2::element_text(color = "black", size = 11 * scale),
+    text = ggplot2::element_text(size = 12 * scale)						# size for all (legend?) labels
+    # legend.key = element_rect(fill = "white")
   )
 
-  pca_plot <- factoextra::fviz_pca_ind(pca, axes = c(dimensionA, dimensionB), invisible = "none", pointsize = pointsize * scale, label = "none", axes.linetype = "blank", repel = FALSE)
+  # show points if neither color- nor shape-groups
+  if (is.null(color.group) && is.null(shape.group)) {
+    invisible <-  "none"
+  } else {
+    invisible <-  "ind"
+    # prepare df for mapping
+    df <- data.frame(x = pca$ind$coord[, dimensionA], y = pca$ind$coord[, dimensionB])
+  }
+
+  pca_plot <- factoextra::fviz_pca_ind(pca, axes = c(dimensionA, dimensionB), invisible = invisible, pointsize = pointsize * scale, label = "none", axes.linetype = "blank", repel = FALSE)
   pca_plot <- pca_plot + theme1
 
-  if(labels) {
+  # grouping
+  scale_color <- NULL
+  scale_shape <- NULL
+  # color points by groups
+  if (is.vector(color.group)) {
+    color.group <- as.factor(color.group)
+    df <- data.frame(df, color = color.group)
+
+    scale_color <- ggplot2::scale_color_manual(
+      values = grDevices::colorRampPalette(palette)(nlevels(color.group)),
+      name = color.title
+    )
+  }
+  # shape points by groups
+  if (is.vector(shape.group)) {
+    shape.group <- as.factor(shape.group)
+    df <- data.frame(df, shape = shape.group)
+
+    scale_shape <- ggplot2::scale_shape_manual(
+      values = rep(shapes, length.out = nlevels(shape.group)),
+      name = shape.title
+    )
+  }
+  # generate mapping
+  if (!is.null(color.group) && !is.null(shape.group)) {
+    mapping <- ggplot2::aes(x = x, y = y, color = color, shape = shape)
+  } else if (!is.null(color.group)) {
+    mapping <- ggplot2::aes(x = x, y = y, color = color)
+  } else if (!is.null(shape.group)) {
+    mapping <- ggplot2::aes(x = x, y = y, shape = shape)
+  }
+  # apply grouping
+  if (!is.null(color.group) || !is.null(shape.group)) {
+    pca_plot <- pca_plot +
+      ggplot2::geom_point(data = df, mapping = mapping, size = pointsize * scale) +
+      scale_color +
+      scale_shape
+  }
+
+  if (labels) {
     pca_plot <- pca_plot + ggrepel::geom_text_repel(
       data = data.frame(pca$ind$coord),
       mapping = ggplot2::aes_(x = pca$ind$coord[, dimensionA], y = pca$ind$coord[, dimensionB], label = rownames(pca$ind$coord)),
@@ -394,8 +448,8 @@ create_pca <- function(data, dimensionA = 1, dimensionB = 2, dimensions = 6, on.
     )
   }
 
-  #ensure quadratic plot
-  # if(width == height){
+  # ensure quadratic plot
+  # if (width == height) {
   #   pca_plot <- pca_plot + ggplot2::coord_fixed(ratio = 1)
   # }
 
@@ -405,11 +459,11 @@ create_pca <- function(data, dimensionA = 1, dimensionB = 2, dimensions = 6, on.
 
   # size exceeded?
   exceed_size <- FALSE
-  if(width > 500) {
+  if (width > 500) {
     exceed_size <- TRUE
     width <- 500
   }
-  if(height > 500) {
+  if (height > 500) {
     exceed_size <- TRUE
     height <- 500
   }
diff --git a/R/pca.R b/R/pca.R
index 5cdc603..d79e587 100644
--- a/R/pca.R
+++ b/R/pca.R
@@ -35,6 +35,10 @@ pcaUI <- function(id, show.label = TRUE) {
             shiny::div(id = ns("guide_dimensions"),
                        shiny::numericInput(ns("dimA"), label = "PCA dimension (x-axis)", min = 1, max = 6, step = 1, value = 1),
                        shiny::numericInput(ns("dimB"), label = "PCA dimension (y-axis)", min = 1, max = 6, step = 1, value = 2)
+            ),
+            shiny::div(id = ns("guide_grouping"),
+                       labelUI(ns("group")),
+                       labelUI(ns("group2"))
             )
           ),
           shiny::column(
@@ -42,6 +46,9 @@ pcaUI <- function(id, show.label = TRUE) {
             shiny::div(id = ns("guide_pointsize"),
                        shiny::sliderInput(ns("pointsize"),label = "Point size", min = 0.1, max = 10, value = 2),
                        shiny::sliderInput(ns("labelsize"), label = "Label size", min = 1, max = 20, value = 5, round = TRUE)
+            ),
+            shiny::div(id = ns("guide_color"),
+                       colorPicker2UI(id = ns("colorPicker"), show.scaleoptions = FALSE, show.transparency = FALSE)
             )
           )
         ),
@@ -127,6 +134,9 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
 
   # modules/ ui #####
   columnSelect <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
+  factor_data <- shiny::callModule(label, "group", label = "Select color grouping factors", data = shiny::reactive(object()$metadata[key %in% columnSelect$selectedColumns(), c(object()$get_factors())]), unique = FALSE)
+  factor_data2 <- shiny::callModule(label, "group2", label = "Select shape grouping factors", data = shiny::reactive(object()$metadata[key %in% columnSelect$selectedColumns(), c(object()$get_factors())]), unique = FALSE)
+  colorPicker <- shiny::callModule(colorPicker2, "colorPicker",  distribution = "categorical", selected = "Dark2")
 
   # update dimension inputs
   shiny::observe({
@@ -152,6 +162,9 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
     shinyjs::reset("pointsize")
     shinyjs::reset("labelsize")
     columnSelect <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
+    factor_data <<- shiny::callModule(label, "group", label = "Select color grouping factors", data = shiny::reactive(object()$metadata[key %in% columnSelect$selectedColumns(), c(object()$get_factors())]), unique = FALSE)
+    factor_data2 <<- shiny::callModule(label, "group2", label = "Select shape grouping factors", data = shiny::reactive(object()$metadata[key %in% columnSelect$selectedColumns(), c(object()$get_factors())]), unique = FALSE)
+    colorPicker <<- shiny::callModule(colorPicker2, "colorPicker",  distribution = "categorical", selected = "Dark2")
     clearPlot(TRUE)
   })
 
@@ -182,6 +195,11 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
 
     plot <- create_pca(
                data = result_data(),
+               color.group = factor_data()$label,
+               color.title = paste0(factor_data()$selected, collapse = ", "),
+               palette = colorPicker()$palette,
+               shape.group = factor_data2()$label,
+               shape.title = paste0(factor_data2()$selected, collapse = ", "),
                dimensionA = input$dimA,
                dimensionB = input$dimB,
                dimensions = length(columnSelect$selectedColumns()) - 1,
@@ -249,14 +267,17 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
     # format selection
     selection <- list(
       data = list(type = columnSelect$type(), selectedColumns = columnSelect$selectedColumns()),
-      dimensions = list(xaxis = input$dimA, yaxis = input$dimB)
+      dimensions = list(xaxis = input$dimA, yaxis = input$dimB),
+      colorGrouping = factor_data()$selected,
+      shapeGrouping = factor_data2()$selected
     )
 
     # format options
     options <- list(
       show_label = input$label,
       pointsize = input$pointsize,
-      labelsize = input$labelsize
+      labelsize = input$labelsize,
+      colorOptions = list(scheme = colorPicker()$name, reverse = colorPicker()$reverse)
     )
 
     # merge all
@@ -264,38 +285,39 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
   })
 
   # notifications #####
-  # insufficient data/ invalid dimension warnings
+  # invalid dimension/ insufficient data warnings
+  # enable/ disable plot button
   shiny::observe({
     shinyjs::enable("plot")
 
-    col_num <- length(shiny::req(columnSelect$selectedColumns()))
-
-    # invalid dimension
-    if (col_num >= 3 && (is.na(input$dimA) || is.na(input$dimB) || input$dimA <= 0 || input$dimA >= col_num || input$dimB <= 0 || input$dimB >= col_num)) {
+    # no selection
+    if (!shiny::isTruthy(columnSelect$selectedColumns())) {
       shinyjs::disable("plot")
-
-      shiny::showNotification(
-        ui = "Invalid dimension(s)! Please select an integer value between 1 and number of selected columns - 1.",
-        id = "dimension",
-        type = "warning"
-      )
     } else {
-      shiny::removeNotification("dimension")
-    }
-
-    # insufficient data
-    if (col_num < 3 || nrow(shiny::isolate(object()$data)) < 3) {
-      shinyjs::disable("plot")
-
-      shiny::showNotification(
-        ui = "Not enough columns/ rows selected! At least 3 of each needed for plotting.",
-        id = "data",
-        type = "warning"
-      )
-
+      col_num <- length(columnSelect$selectedColumns())
+      # insufficient data
+      if (col_num < 3 || nrow(shiny::isolate(object()$data)) < 3) {
+        shinyjs::disable("plot")
+        shiny::showNotification(
+          ui = "Not enough columns/ rows selected! At least 3 of each needed for plotting.",
+          id = session$ns("data"),
+          type = "warning"
+        )
+      } else {
+        shiny::removeNotification(session$ns("data"))
+      }
 
-    } else {
-      shiny::removeNotification("data")
+      # invalid dimension
+      if (col_num >= 3 && (is.na(input$dimA) || is.na(input$dimB) || input$dimA <= 0 || input$dimA >= col_num || input$dimB <= 0 || input$dimB >= col_num)) {
+        shinyjs::disable("plot")
+        shiny::showNotification(
+          ui = "Invalid dimension(s)! Please select an integer value between 1 and number of selected columns - 1.",
+          id = session$ns("dimension"),
+          type = "warning"
+        )
+      } else {
+        shiny::removeNotification(session$ns("dimension"))
+      }
     }
   })
 
@@ -304,11 +326,11 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
     if (plot()$exceed_size) {
       shiny::showNotification(
         ui = "Width and/ or height exceed limit. Using 500 cm instead.",
-        id = "limit",
+        id = session$ns("limit"),
         type = "warning"
       )
     } else {
-      shiny::removeNotification("limit")
+      shiny::removeNotification(session$ns("limit"))
     }
   })
 
@@ -334,8 +356,13 @@ pcaGuide <- function(session) {
     "guide_dimensions" = "<h4>PCA dimensions</h4>
     Choose which PCA dimensions are shown on the x-axis and y-axis.<br/>
     The number of PCA dimensions available for visualization is one less than the number of selected columns in the previous step.",
+    "guide_grouping" = "<h4>Grouping</h4>
+    Use the provided factor(s) to show groups based on colors and/ or shapes of the datapoints.<br/>
+    Multi-factor selections will be merged and evaluated as a single factor.",
     "guide_pointsize" = "<h4>Additional options</h4>
     You can increase or decrease the point size by dragging the slider to the right or to the left. The same goes for the label size and it's respecting slider.",
+    "guide_color" = "<h4>Color palettes</h4>
+    Choose a color palette used for color grouping. The selected pallette can also be reversed.",
     "guide_buttons" = "<h4>Create the plot</h4>
     As a final step, a click on the 'Plot' button will render the plot, while a click on the 'Reset' button will reset the parameters to default."
   )
diff --git a/exec/pca_example.R b/exec/pca_example.R
index 7299b69..90a5bb9 100644
--- a/exec/pca_example.R
+++ b/exec/pca_example.R
@@ -6,11 +6,14 @@ source("../R/function.R")
 source("../R/pca.R")
 source("../R/global.R")
 source("../R/clarion.R")
+source("../R/label.R")
+source("../R/colorPicker2.R")
+source("../R/limit.R")
 
 ####Test Data
 data <- data.table::as.data.table(mtcars, keep.rowname = "id")
 # create metadata
-metadata <- data.table::data.table(names(data), level = c("feature", rep("sample", 7), rep("condition", 4)))
+metadata <- data.table::data.table(names(data), level = c("feature", rep("sample", 7), rep("condition", 4)), factor1 = c(rep("group_a", 6), rep("group_b", 6)), factor2 = c(rep("group_1", 3), rep("group_2", 3), rep("group_3", 6)))
 names(metadata)[1] <- "key"
 clarion <- Clarion$new(data = data, metadata = metadata)
 ####
diff --git a/man/create_pca.Rd b/man/create_pca.Rd
index fbb0e70..74b7f83 100644
--- a/man/create_pca.Rd
+++ b/man/create_pca.Rd
@@ -4,14 +4,27 @@
 \alias{create_pca}
 \title{Method for pca creation.}
 \usage{
-create_pca(data, dimensionA = 1, dimensionB = 2, dimensions = 6,
-  on.columns = TRUE, labels = FALSE, custom.labels = NULL,
-  pointsize = 2, labelsize = 3, width = 28, height = 28, ppi = 72,
-  scale = 1)
+create_pca(data, color.group = NULL, color.title = NULL, palette = NULL,
+  shape.group = NULL, shape.title = NULL, shapes = c(15:25),
+  dimensionA = 1, dimensionB = 2, dimensions = 6, on.columns = TRUE,
+  labels = FALSE, custom.labels = NULL, pointsize = 2, labelsize = 3,
+  width = 28, height = 28, ppi = 72, scale = 1)
 }
 \arguments{
 \item{data}{data.table from which the plot is created (First column will be handled as rownames if not numeric).}
 
+\item{color.group}{Vector of groups according to samples (= column names).}
+
+\item{color.title}{Title of the color legend.}
+
+\item{palette}{Vector of colors used for color palette.}
+
+\item{shape.group}{Vector of groups according to samples (= column names).}
+
+\item{shape.title}{Title of the shape legend.}
+
+\item{shapes}{Vector of shapes see \code{\link[graphics]{points}}. Will recycle/ cut off shapes if needed. Default = c(15:25)}
+
 \item{dimensionA}{Number of dimension displayed on X-Axis.}
 
 \item{dimensionB}{Number of dimension displayed on Y-Axis.}

From 0e12c11e6fa1bcf4ba9bbbf012e5fa799731d17e Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 24 May 2018 14:17:28 +0200
Subject: [PATCH 23/75] added missing session$ns() to notifications

---
 R/geneView.R           | 8 ++++----
 R/global_cor_heatmap.R | 8 ++++----
 R/heatmap.R            | 8 ++++----
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/R/geneView.R b/R/geneView.R
index bf45a95..63ab75b 100644
--- a/R/geneView.R
+++ b/R/geneView.R
@@ -365,11 +365,11 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
         paste("Caution! You selected", length(input$genes), "genes. This may take a while to compute."),
         duration = 5,
         type = "warning",
-        id = "warning",
+        id = session$ns("warning"),
         closeButton = FALSE
       )
     }else{
-      shiny::removeNotification("warning")
+      shiny::removeNotification(session$ns("warning"))
     }
   })
 
@@ -378,11 +378,11 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
     if (plot()$exceed_size) {
       shiny::showNotification(
         ui = "Width and/ or height exceed limit. Using 500 cm instead.",
-        id = "limit",
+        id = session$ns("limit"),
         type = "warning"
       )
     } else {
-      shiny::removeNotification("limit")
+      shiny::removeNotification(session$ns("limit"))
     }
   })
   # Fetch the reactive guide for this module
diff --git a/R/global_cor_heatmap.R b/R/global_cor_heatmap.R
index 5c51f72..b97bbf7 100644
--- a/R/global_cor_heatmap.R
+++ b/R/global_cor_heatmap.R
@@ -245,11 +245,11 @@ global_cor_heatmap <- function(input, output, session, clarion, plot.method = "s
     if (plot()$exceed_size) {
       shiny::showNotification(
         ui = "Width and/ or height exceed limit. Using 500 cm instead.",
-        id = "limit",
+        id = session$ns("limit"),
         type = "warning"
       )
     } else {
-      shiny::removeNotification("limit")
+      shiny::removeNotification(session$ns("limit"))
     }
   })
 
@@ -266,11 +266,11 @@ global_cor_heatmap <- function(input, output, session, clarion, plot.method = "s
     if (length(columns$selectedColumns()) < 2) {
       shiny::showNotification(
         ui = "Warning! At least two columns needed. Please select more.",
-        id = "less_data_warning",
+        id = session$ns("less_data_warning"),
         type = "warning"
       )
     } else {
-      shiny::removeNotification("less_data_warning")
+      shiny::removeNotification(session$ns("less_data_warning"))
     }
   })
 
diff --git a/R/heatmap.R b/R/heatmap.R
index c0a279b..c9d909b 100644
--- a/R/heatmap.R
+++ b/R/heatmap.R
@@ -353,11 +353,11 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
       if (show_warning) {
         shiny::showNotification(
           ui = "Warning! Insufficient columns/ rows. Either disable the respective clustering or expand the dataset.",
-          id = "insuf_data",
+          id = session$ns("insuf_data"),
           type = "warning"
         )
       } else {
-        shiny::removeNotification("insuf_data")
+        shiny::removeNotification(session$ns("insuf_data"))
       }
 
       # maximum heatmap reached?
@@ -413,11 +413,11 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
     if (plot()$exceed_size) {
       shiny::showNotification(
         ui = "Width and/ or height exceed limit. Using 500 cm instead.",
-        id = "limit",
+        id = session$ns("limit"),
         type = "warning"
       )
     } else {
-      shiny::removeNotification("limit")
+      shiny::removeNotification(session$ns("limit"))
     }
   })
 

From 0cb954d4a4fb39ad809d0660155281af0651848c Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Tue, 29 May 2018 11:55:28 +0200
Subject: [PATCH 24/75] param grouping deprecated

---
 R/featureSelector.R         | 2 +-
 man/featureSelectorGuide.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/featureSelector.R b/R/featureSelector.R
index ad4f7d8..9d15d95 100644
--- a/R/featureSelector.R
+++ b/R/featureSelector.R
@@ -325,7 +325,7 @@ featureSelector <- function(input, output, session, clarion, multiple = TRUE, co
 #'
 #' @return A shiny reactive that contains the texts for the guide steps.
 #'
-featureSelectorGuide <- function(session, grouping = FALSE) {
+featureSelectorGuide <- function(session) {
   steps <- list("guide_and" = "<h4>Grouping</h4>
       These boxes contain several selectors each.<br/>
       Expand/ Collapse them with a click on the '+'/ '-' on the right side.<br/>
diff --git a/man/featureSelectorGuide.Rd b/man/featureSelectorGuide.Rd
index 77e27be..0871913 100644
--- a/man/featureSelectorGuide.Rd
+++ b/man/featureSelectorGuide.Rd
@@ -4,7 +4,7 @@
 \alias{featureSelectorGuide}
 \title{featureSelector module guide}
 \usage{
-featureSelectorGuide(session, grouping = FALSE)
+featureSelectorGuide(session)
 }
 \arguments{
 \item{session}{The shiny session}

From 32524797605c5f2de3817d91f9e8cd81dde73ea7 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Mon, 4 Jun 2018 14:19:17 +0200
Subject: [PATCH 25/75] clarion: accept factor names e.g. factor1="name"

---
 R/clarion.R | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/R/clarion.R b/R/clarion.R
index 61922b8..d909555 100644
--- a/R/clarion.R
+++ b/R/clarion.R
@@ -49,7 +49,23 @@ Clarion <- R6::R6Class("Clarion",
                            }
                          },
                          get_factors = function() {
-                           grep("^factor\\d+", names(self$metadata), perl = TRUE, value = TRUE)
+                           # returns data.table key(, factor columns)
+                           # only name for named factors (e.g. factor1="name")
+
+                           # get factor columns
+                           columns <- grep("^factor\\d+", names(self$metadata), perl = TRUE, value = TRUE)
+                           # on no factors return key column
+                           if (length(columns) == 0) return(self$metadata[, "key"])
+
+                           # extract names
+                           ext_names <- sub("^factor\\d+=\"(.*)\"", replacement = "\\1", columns, perl = TRUE)
+
+                           # get factor table
+                           factor_table <- self$metadata[, c("key", columns), with = FALSE]
+                           # rename columns
+                           names(factor_table)[-1] <- ext_names
+
+                           return(factor_table)
                          },
                          validate = function() {
                            # validate header
@@ -103,7 +119,7 @@ Clarion <- R6::R6Class("Clarion",
                          ## metadata checks
                          check_metadataHeader = function() {
                            # case: invalid column names
-                           valid_names <- c("key", "factor\\d+", "level", "type", "label", "sub_label")
+                           valid_names <- c("key", "factor\\d+(=\".*\")?", "level", "type", "label", "sub_label")
                            regex <- paste0("^", valid_names, "$", collapse = "|")
                            invalid_names <- grep(regex, names(self$metadata), invert = TRUE, value = TRUE, perl = TRUE)
                            if (length(invalid_names) > 0) {

From 7faf2632015c7cd7415998dbe632b2bf0e078049 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Mon, 4 Jun 2018 14:19:40 +0200
Subject: [PATCH 26/75] geneview, pca: updated to use factor names

---
 R/geneView.R | 4 ++--
 R/pca.R      | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/geneView.R b/R/geneView.R
index 63ab75b..928fdf3 100644
--- a/R/geneView.R
+++ b/R/geneView.R
@@ -146,7 +146,7 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
   transform <- shiny::callModule(transformation, "transform", shiny::reactive(as.matrix(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes), selector$selectedColumns(), with = FALSE])))
   selector <- shiny::callModule(columnSelector, "selector", type.columns = shiny::reactive(object()$metadata[level != "feature", c("key", "level")]), columnTypeLabel = "Select Columns")
   custom_label <- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes)]), sep = label.sep)
-  factor_data <- shiny::callModule(label, "group", label = "Select grouping factors", data = shiny::reactive(object()$metadata[key %in% selector$selectedColumns(), c(object()$get_factors())]), sep = label.sep, unique = FALSE)
+  factor_data <- shiny::callModule(label, "group", label = "Select grouping factors", data = shiny::reactive(object()$get_factors()[key %in% selector$selectedColumns(), !"key"]), sep = label.sep, unique = FALSE)
   limiter <- shiny::callModule(limit, "limit", lower = shiny::reactive(get_limits()[1]), upper = shiny::reactive(get_limits()[2]))
 
   output$genes <- shiny::renderUI({
@@ -185,7 +185,7 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
     transform <<- shiny::callModule(transformation, "transform", shiny::reactive(as.matrix(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes), selector$selectedColumns(), with = FALSE])))
     selector <<- shiny::callModule(columnSelector, "selector", type.columns = shiny::reactive(object()$metadata[level != "feature", c("key", "level")]), columnTypeLabel = "Select Columns")
     custom_label <<- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes)]), sep = label.sep)
-    factor_data <<- shiny::callModule(label, "group", label = "Select grouping factors", data = shiny::reactive(object()$metadata[key %in% selector$selectedColumns(), c(object()$get_factors())]), sep = label.sep, unique = FALSE)
+    factor_data <<- shiny::callModule(label, "group", label = "Select grouping factors", data = shiny::reactive(object()$get_factors()[key %in% selector$selectedColumns(), !"key"]), sep = label.sep, unique = FALSE)
     limiter <<- shiny::callModule(limit, "limit", lower = shiny::reactive(get_limits()[1]), upper = shiny::reactive(get_limits()[2]))
     clearPlot(TRUE)
   })
diff --git a/R/pca.R b/R/pca.R
index d79e587..2f776ee 100644
--- a/R/pca.R
+++ b/R/pca.R
@@ -134,8 +134,8 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
 
   # modules/ ui #####
   columnSelect <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
-  factor_data <- shiny::callModule(label, "group", label = "Select color grouping factors", data = shiny::reactive(object()$metadata[key %in% columnSelect$selectedColumns(), c(object()$get_factors())]), unique = FALSE)
-  factor_data2 <- shiny::callModule(label, "group2", label = "Select shape grouping factors", data = shiny::reactive(object()$metadata[key %in% columnSelect$selectedColumns(), c(object()$get_factors())]), unique = FALSE)
+  factor_data <- shiny::callModule(label, "group", label = "Select color grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columnSelect$selectedColumns(), !"key"]), unique = FALSE)
+  factor_data2 <- shiny::callModule(label, "group2", label = "Select shape grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columnSelect$selectedColumns(), !"key"]), unique = FALSE)
   colorPicker <- shiny::callModule(colorPicker2, "colorPicker",  distribution = "categorical", selected = "Dark2")
 
   # update dimension inputs
@@ -162,8 +162,8 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
     shinyjs::reset("pointsize")
     shinyjs::reset("labelsize")
     columnSelect <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
-    factor_data <<- shiny::callModule(label, "group", label = "Select color grouping factors", data = shiny::reactive(object()$metadata[key %in% columnSelect$selectedColumns(), c(object()$get_factors())]), unique = FALSE)
-    factor_data2 <<- shiny::callModule(label, "group2", label = "Select shape grouping factors", data = shiny::reactive(object()$metadata[key %in% columnSelect$selectedColumns(), c(object()$get_factors())]), unique = FALSE)
+    factor_data <<- shiny::callModule(label, "group", label = "Select color grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columnSelect$selectedColumns(), !"key"]), unique = FALSE)
+    factor_data2 <<- shiny::callModule(label, "group2", label = "Select shape grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columnSelect$selectedColumns(), !"key"]), unique = FALSE)
     colorPicker <<- shiny::callModule(colorPicker2, "colorPicker",  distribution = "categorical", selected = "Dark2")
     clearPlot(TRUE)
   })

From ca2b1bedd94eea0f0d7cc1cd008aff2fbbd66da0 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Mon, 18 Jun 2018 10:02:13 +0200
Subject: [PATCH 27/75] closeButton for all notifications

---
 R/geneView.R | 3 +--
 R/heatmap.R  | 9 +++------
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/R/geneView.R b/R/geneView.R
index 928fdf3..1f8fdfe 100644
--- a/R/geneView.R
+++ b/R/geneView.R
@@ -365,8 +365,7 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
         paste("Caution! You selected", length(input$genes), "genes. This may take a while to compute."),
         duration = 5,
         type = "warning",
-        id = session$ns("warning"),
-        closeButton = FALSE
+        id = session$ns("warning")
       )
     }else{
       shiny::removeNotification(session$ns("warning"))
diff --git a/R/heatmap.R b/R/heatmap.R
index c9d909b..e685e0a 100644
--- a/R/heatmap.R
+++ b/R/heatmap.R
@@ -378,16 +378,14 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
             paste("Clustering limited to", static, "genes! Please disable clustering or select less genes."),
             duration = NULL,
             type = "error",
-            id = session$ns("notification"),
-            closeButton = FALSE
+            id = session$ns("notification")
           )
         } else if (plot.method == "interactive" && nrow(object()$data) > interactive) { # cluster limitation (interactive)
           shiny::showNotification(
             paste("Clustering limited to", interactive, "genes! Please disable clustering or select less genes."),
             duration = NULL,
             type = "error",
-            id = session$ns("notification"),
-            closeButton = FALSE
+            id = session$ns("notification")
           )
         } else {
           shiny::removeNotification(session$ns("notification"))
@@ -397,8 +395,7 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
           paste("Caution! You selected", nrow(object()$data), "genes. This will take a while to compute."),
           duration = 5,
           type = "warning",
-          id = session$ns("notification"),
-          closeButton = FALSE
+          id = session$ns("notification")
         )
       } else {
         shiny::removeNotification(session$ns("notification"))

From 5dcf4e232a38e75793385b402894af1822529372 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Mon, 18 Jun 2018 10:07:15 +0200
Subject: [PATCH 28/75] added function docu

---
 man/forceArgs.Rd | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 man/forceArgs.Rd

diff --git a/man/forceArgs.Rd b/man/forceArgs.Rd
new file mode 100644
index 0000000..5c83a7b
--- /dev/null
+++ b/man/forceArgs.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/function.R
+\name{forceArgs}
+\alias{forceArgs}
+\title{Force evaluation of the parent function's arguments.}
+\usage{
+forceArgs(args)
+}
+\arguments{
+\item{args}{List of Argument names to force evaluation. Defaults to all named arguments see \code{\link[base]{match.call}}.}
+}
+\description{
+Force evaluation of the parent function's arguments.
+}
+\details{
+Similar to \code{\link[base]{forceAndCall}} but used from within the respective function.
+
+This method is not using \code{\link[base]{force}} as it is restricted to it's calling environment. Instead \code{\link[base]{get}} is used.
+}

From e74a29d06688f31d6633a830523e0f57e7eac434 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Mon, 18 Jun 2018 12:47:25 +0200
Subject: [PATCH 29/75] clarion: enhanced docu; fixed examples

---
 R/clarion.R    | 30 ++++++++++++++++++++++++++++++
 man/Clarion.Rd | 40 ++++++++++++++++++++++++++++++++++++----
 2 files changed, 66 insertions(+), 4 deletions(-)

diff --git a/R/clarion.R b/R/clarion.R
index d909555..5d0d990 100644
--- a/R/clarion.R
+++ b/R/clarion.R
@@ -3,18 +3,48 @@
 #' Use this to create a clarion object.
 #' This object is used by all top-level wilson modules.
 #'
+#' @section Methods:
+#' \describe{
+#'     \item{\code{get_uniqueID()}}{
+#'       Returns name of unique column. Assumes first feature to be unique if not specified.
+#'     }
+#'     \item{\code{get_name()}}{
+#'       Returns name of name column. If not specified return unique Id.
+#'     }
+#'     \item{\code{get_delimiter()}}{
+#'       Return delimiter used within multi-value fields (no delimiter = NULL).
+#'     }
+#'     \item{\code{is_delimited(x)}}{
+#'       Logical whether the given column name is delimited.
+#'     }
+#'     \item{\code{get_factors()}}{
+#'       Returns a data.table columns: key and factor(s) if any. Named factors (e.g. factor1="name") will be cropped to their name.
+#'     }
+#'     \item{\code{validate()}}{
+#'       Check the object for inconsistencies.
+#'     }
+#'   }
+#'
 #' @param header A named list. Defaults to NULL.
 #' @param metadata Clarion metadata in form of a data.table.
 #' @param data Data.table according to metadata.
 #' @param validate Logical value to validate on initialization. Defaults to TRUE.
 #'
+#' @field header List of global information regarding the whole experiment.
+#' @field metadata Data.table with additional information for each column.
+#' @field data Data.table containing experiment result data.
+#'
 #' @examples
+#' \dontrun{
 #' # initializing a new object
 #' object <- Clarion$new(header, metadata, data, validate = TRUE)
 #'
 #' # create a deep copy
 #' object_copy <- object$clone(deep = TRUE)
+#' }
 #'
+#' @format NULL
+#' @usage NULL
 #' @export
 Clarion <- R6::R6Class("Clarion",
                        public = list(
diff --git a/man/Clarion.Rd b/man/Clarion.Rd
index f02070a..9b4e4fa 100644
--- a/man/Clarion.Rd
+++ b/man/Clarion.Rd
@@ -4,10 +4,6 @@
 \name{Clarion}
 \alias{Clarion}
 \title{Clarion R6-class definition}
-\format{An object of class \code{R6ClassGenerator} of length 24.}
-\usage{
-Clarion
-}
 \arguments{
 \item{header}{A named list. Defaults to NULL.}
 
@@ -21,12 +17,48 @@ Clarion
 Use this to create a clarion object.
 This object is used by all top-level wilson modules.
 }
+\section{Fields}{
+
+\describe{
+\item{\code{header}}{List of global information regarding the whole experiment.}
+
+\item{\code{metadata}}{Data.table with additional information for each column.}
+
+\item{\code{data}}{Data.table containing experiment result data.}
+}}
+
+\section{Methods}{
+
+\describe{
+    \item{\code{get_uniqueID()}}{
+      Returns name of unique column. Assumes first feature to be unique if not specified.
+    }
+    \item{\code{get_name()}}{
+      Returns name of name column. If not specified return unique Id.
+    }
+    \item{\code{get_delimiter()}}{
+      Return delimiter used within multi-value fields (no delimiter = NULL).
+    }
+    \item{\code{is_delimited(x)}}{
+      Logical whether the given column name is delimited.
+    }
+    \item{\code{get_factors()}}{
+      Returns a data.table columns: key and factor(s) if any. Named factors (e.g. factor1="name") will be cropped to their name.
+    }
+    \item{\code{validate()}}{
+      Check the object for inconsistencies.
+    }
+  }
+}
+
 \examples{
+\dontrun{
 # initializing a new object
 object <- Clarion$new(header, metadata, data, validate = TRUE)
 
 # create a deep copy
 object_copy <- object$clone(deep = TRUE)
+}
 
 }
 \keyword{datasets}

From f4015033f610182720750faf78e74db2a07d961d Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Tue, 19 Jun 2018 12:55:50 +0200
Subject: [PATCH 30/75] satisfy R cmd check by using SE approaches for ggplot
 related variables and utils::globalVariables() in terms of data.table

---
 R/function.R | 20 ++++++++++----------
 R/zzz.R      | 12 ++++++++++++
 2 files changed, 22 insertions(+), 10 deletions(-)

diff --git a/R/function.R b/R/function.R
index d63667a..8e82ba7 100644
--- a/R/function.R
+++ b/R/function.R
@@ -125,7 +125,7 @@ create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL,
   if (density) {
     ### kernel density
     # plot$layers <- c(stat_density2d(geom = "tile", aes(fill = ..density..^0.25), n=200, contour=FALSE) + aes_(fill = as.name(var)), plot$layers) # n = resolution; density less sparse
-    plot <- plot + ggplot2::stat_density2d(geom = "tile", ggplot2::aes(fill = ..density..^0.25), n = 200, contour = FALSE)
+    plot <- plot + ggplot2::stat_density2d(geom = "tile", ggplot2::aes_(fill = ~ ..density..^0.25), n = 200, contour = FALSE)
 
     plot <- plot + ggplot2::scale_fill_gradient(low = "white", high = "black") +
       # guides(fill=FALSE) +		# remove density legend
@@ -429,11 +429,11 @@ create_pca <- function(data, color.group = NULL, color.title = NULL, palette = N
   }
   # generate mapping
   if (!is.null(color.group) && !is.null(shape.group)) {
-    mapping <- ggplot2::aes(x = x, y = y, color = color, shape = shape)
+    mapping <- ggplot2::aes_string(x = "x", y = "y", color = "color", shape = "shape")
   } else if (!is.null(color.group)) {
-    mapping <- ggplot2::aes(x = x, y = y, color = color)
+    mapping <- ggplot2::aes_string(x = "x", y = "y", color = "color")
   } else if (!is.null(shape.group)) {
-    mapping <- ggplot2::aes(x = x, y = y, shape = shape)
+    mapping <- ggplot2::aes_string(x = "x", y = "y", shape = "shape")
   }
   # apply grouping
   if (!is.null(color.group) || !is.null(shape.group)) {
@@ -904,7 +904,7 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
       matrixplot = matrixplot + ggplot2::aes(x = condition, fill = condition)
 
       if (plot.type == "line") {													#line plot: no facetting, different size algorithm
-        matrixplot <- matrixplot + ggplot2::aes(x = variable, colour = condition, group = condition, fill = NULL)
+        matrixplot <- matrixplot + ggplot2::aes_(x = ~ variable, colour = ~ condition, group = ~ condition, fill = NULL)
         matrixplot <- matrixplot + ggplot2::scale_x_discrete(expand = c(0.05, 0.05))								#expand to reduce the whitespace inside the plot (left/right)
       } else {
         #compute number of rows to get facet.cols columns (works better with plotly)
@@ -914,10 +914,10 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
       }
     }
     if (facet.target == "condition") {													#facet = condition
-      matrixplot <- matrixplot + ggplot2::aes(x = variable, fill = variable)
+      matrixplot <- matrixplot + ggplot2::aes_(x = ~ variable, fill = ~ variable)
 
       if (plot.type == "line") {													#line plot: no facetting, different size algorithm
-        matrixplot <- matrixplot + ggplot2::aes(x = condition, colour = variable, group = variable, fill = NULL)
+        matrixplot <- matrixplot + ggplot2::aes_(x = ~ condition, colour = ~ variable, group = ~ variable, fill = NULL)
         matrixplot <- matrixplot + ggplot2::scale_x_discrete(expand = c(0.05,0.05))								#expand to reduce the whitespace inside the plot (left/right)
       } else {
         #compute number of rows to get facet.cols columns (works better with plotly)
@@ -948,7 +948,7 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
     if (plot.type == "line") {
       matrixplot <- matrixplot + ggplot2::theme(legend.position = "right")
       #matrixplot <- matrixplot + geom_errorbar(aes(ymin = value-sd, ymax = value + sd), width = 0.05)								#error bar = standard deviation
-      matrixplot <- matrixplot + ggplot2::geom_errorbar(ggplot2::aes(ymin = value - se, ymax = value + se), size = 0.2, width = 0.05)								#error bar = standard error
+      matrixplot <- matrixplot + ggplot2::geom_errorbar(ggplot2::aes_(ymin = ~ value - se, ymax = ~ value + se), size = 0.2, width = 0.05)								#error bar = standard error
       matrixplot <- matrixplot + ggplot2::geom_line() + ggplot2::geom_point()											#bar plot of the mean (color=condition)
       #set hovertext
       matrixplot <- matrixplot + ggplot2::aes(text = paste("ID: ", data$variable, "\n",
@@ -1270,8 +1270,8 @@ download <- function(file, filename, plot, width, height, ppi = 72, save_plot =
   if (save_plot) {
     # create temp file name
     plot_object_file <- tempfile(pattern = "plot_object", fileext = ".RData")
-    ggplot2_version <- as.character(packageVersion("ggplot2"))
-    plotly_version <- as.character(packageVersion("plotly"))
+    ggplot2_version <- as.character(utils::packageVersion("ggplot2"))
+    plotly_version <- as.character(utils::packageVersion("plotly"))
     r_version <- R.Version()$version.string
 
     save(plot, ggplot2_version, plotly_version, r_version, file = plot_object_file)
diff --git a/R/zzz.R b/R/zzz.R
index 24d61b2..548299f 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -2,3 +2,15 @@
   # make server aware of images
   shiny::addResourcePath(prefix = "wilson_www", directoryPath = system.file("www", package = "wilson"))
 }
+
+# hideous hack
+# set variables otherwise noted by R cmd check 'no visible binding for...'
+utils::globalVariables(
+  c(
+    "Experiment",
+    "col_name",
+    "condition",
+    "level",
+    "type"
+  )
+)

From 65d57a7d2bbbb16daccfe805760f0493f426a987 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Tue, 19 Jun 2018 12:55:50 +0200
Subject: [PATCH 31/75] satisfy R cmd check by using SE approaches for ggplot
 related variables and utils::globalVariables() in terms of data.table

---
 R/function.R | 20 ++++++++++----------
 R/zzz.R      | 14 ++++++++++++++
 2 files changed, 24 insertions(+), 10 deletions(-)

diff --git a/R/function.R b/R/function.R
index d63667a..8e82ba7 100644
--- a/R/function.R
+++ b/R/function.R
@@ -125,7 +125,7 @@ create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL,
   if (density) {
     ### kernel density
     # plot$layers <- c(stat_density2d(geom = "tile", aes(fill = ..density..^0.25), n=200, contour=FALSE) + aes_(fill = as.name(var)), plot$layers) # n = resolution; density less sparse
-    plot <- plot + ggplot2::stat_density2d(geom = "tile", ggplot2::aes(fill = ..density..^0.25), n = 200, contour = FALSE)
+    plot <- plot + ggplot2::stat_density2d(geom = "tile", ggplot2::aes_(fill = ~ ..density..^0.25), n = 200, contour = FALSE)
 
     plot <- plot + ggplot2::scale_fill_gradient(low = "white", high = "black") +
       # guides(fill=FALSE) +		# remove density legend
@@ -429,11 +429,11 @@ create_pca <- function(data, color.group = NULL, color.title = NULL, palette = N
   }
   # generate mapping
   if (!is.null(color.group) && !is.null(shape.group)) {
-    mapping <- ggplot2::aes(x = x, y = y, color = color, shape = shape)
+    mapping <- ggplot2::aes_string(x = "x", y = "y", color = "color", shape = "shape")
   } else if (!is.null(color.group)) {
-    mapping <- ggplot2::aes(x = x, y = y, color = color)
+    mapping <- ggplot2::aes_string(x = "x", y = "y", color = "color")
   } else if (!is.null(shape.group)) {
-    mapping <- ggplot2::aes(x = x, y = y, shape = shape)
+    mapping <- ggplot2::aes_string(x = "x", y = "y", shape = "shape")
   }
   # apply grouping
   if (!is.null(color.group) || !is.null(shape.group)) {
@@ -904,7 +904,7 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
       matrixplot = matrixplot + ggplot2::aes(x = condition, fill = condition)
 
       if (plot.type == "line") {													#line plot: no facetting, different size algorithm
-        matrixplot <- matrixplot + ggplot2::aes(x = variable, colour = condition, group = condition, fill = NULL)
+        matrixplot <- matrixplot + ggplot2::aes_(x = ~ variable, colour = ~ condition, group = ~ condition, fill = NULL)
         matrixplot <- matrixplot + ggplot2::scale_x_discrete(expand = c(0.05, 0.05))								#expand to reduce the whitespace inside the plot (left/right)
       } else {
         #compute number of rows to get facet.cols columns (works better with plotly)
@@ -914,10 +914,10 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
       }
     }
     if (facet.target == "condition") {													#facet = condition
-      matrixplot <- matrixplot + ggplot2::aes(x = variable, fill = variable)
+      matrixplot <- matrixplot + ggplot2::aes_(x = ~ variable, fill = ~ variable)
 
       if (plot.type == "line") {													#line plot: no facetting, different size algorithm
-        matrixplot <- matrixplot + ggplot2::aes(x = condition, colour = variable, group = variable, fill = NULL)
+        matrixplot <- matrixplot + ggplot2::aes_(x = ~ condition, colour = ~ variable, group = ~ variable, fill = NULL)
         matrixplot <- matrixplot + ggplot2::scale_x_discrete(expand = c(0.05,0.05))								#expand to reduce the whitespace inside the plot (left/right)
       } else {
         #compute number of rows to get facet.cols columns (works better with plotly)
@@ -948,7 +948,7 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
     if (plot.type == "line") {
       matrixplot <- matrixplot + ggplot2::theme(legend.position = "right")
       #matrixplot <- matrixplot + geom_errorbar(aes(ymin = value-sd, ymax = value + sd), width = 0.05)								#error bar = standard deviation
-      matrixplot <- matrixplot + ggplot2::geom_errorbar(ggplot2::aes(ymin = value - se, ymax = value + se), size = 0.2, width = 0.05)								#error bar = standard error
+      matrixplot <- matrixplot + ggplot2::geom_errorbar(ggplot2::aes_(ymin = ~ value - se, ymax = ~ value + se), size = 0.2, width = 0.05)								#error bar = standard error
       matrixplot <- matrixplot + ggplot2::geom_line() + ggplot2::geom_point()											#bar plot of the mean (color=condition)
       #set hovertext
       matrixplot <- matrixplot + ggplot2::aes(text = paste("ID: ", data$variable, "\n",
@@ -1270,8 +1270,8 @@ download <- function(file, filename, plot, width, height, ppi = 72, save_plot =
   if (save_plot) {
     # create temp file name
     plot_object_file <- tempfile(pattern = "plot_object", fileext = ".RData")
-    ggplot2_version <- as.character(packageVersion("ggplot2"))
-    plotly_version <- as.character(packageVersion("plotly"))
+    ggplot2_version <- as.character(utils::packageVersion("ggplot2"))
+    plotly_version <- as.character(utils::packageVersion("plotly"))
     r_version <- R.Version()$version.string
 
     save(plot, ggplot2_version, plotly_version, r_version, file = plot_object_file)
diff --git a/R/zzz.R b/R/zzz.R
index 24d61b2..ffc2441 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -2,3 +2,17 @@
   # make server aware of images
   shiny::addResourcePath(prefix = "wilson_www", directoryPath = system.file("www", package = "wilson"))
 }
+
+# hideous hack
+# set variables otherwise noted by R cmd check 'no visible binding for...'
+if (getRversion() >= "2.15.1") {
+  utils::globalVariables(
+    c(
+      "Experiment",
+      "col_name",
+      "condition",
+      "level",
+      "type"
+    )
+  )
+}

From 81f0d266807ba3b72868ddc1ccf9d4716e34e726 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 20 Jun 2018 08:14:08 +0200
Subject: [PATCH 32/75] geneview: violin plot warning

---
 R/geneView.R | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/R/geneView.R b/R/geneView.R
index 1f8fdfe..16ff9b3 100644
--- a/R/geneView.R
+++ b/R/geneView.R
@@ -331,6 +331,7 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
   # enable plot button only if plot possible
   shiny::observe({
     if (is.null(input$genes) || !shiny::isTruthy(selector$selectedColumns())) {
+      shiny::removeNotification(session$ns("violin"))
       shinyjs::disable("plot")
     }else if (input$plotType == "violin") {
       factor_levels <- table(droplevels(as.factor(factor_data()$label), exclude = ""))
@@ -339,19 +340,34 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
         # every level >= 3 times
         factor_levels <- ifelse(length(factor_levels) > 0, factor_levels, FALSE)
         if (all(factor_levels >= 3)) {
+          shiny::removeNotification(session$ns("violin"))
           shinyjs::enable("plot")
         } else {
+          shiny::showNotification(
+            paste("Violin plot not feasible. Insufficient data. Please try a boxplot instead."),
+            duration = 5,
+            type = "warning",
+            id = session$ns("violin")
+          )
           shinyjs::disable("plot")
         }
       } else if (input$groupby == "gene") {
         # at least one level >= 3 times
         if (any(factor_levels >= 3)) {
+          shiny::removeNotification(session$ns("violin"))
           shinyjs::enable("plot")
         } else {
+          shiny::showNotification(
+            paste("Violin plot not feasible. Insufficient data. Please try a boxplot instead."),
+            duration = 5,
+            type = "warning",
+            id = session$ns("violin")
+          )
           shinyjs::disable("plot")
         }
       }
     } else {
+      shiny::removeNotification(session$ns("violin"))
       shinyjs::enable("plot")
     }
   })

From d97b0deff380feb982c66656110036b34d16eae2 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 20 Jun 2018 09:14:31 +0200
Subject: [PATCH 33/75] replaced colorPicker with colorPicker2

---
 DESCRIPTION                       |   1 -
 NAMESPACE                         |   2 -
 R/colorPicker.R                   | 256 +++++++++++++++++++++++++----
 R/colorPicker2.R                  | 262 ------------------------------
 R/geneView.R                      |   6 +-
 R/global_cor_heatmap.R            |   6 +-
 R/heatmap.R                       |   6 +-
 R/marker.R                        |   4 +-
 R/pca.R                           |   6 +-
 R/scatterPlot.R                   |   6 +-
 exec/colorPicker2_example.R       |  33 ----
 exec/colorPicker_example.R        |  24 ++-
 exec/geneView_example.R           |   2 +-
 exec/global_cor_heatmap_example.R |   2 +-
 exec/heatmap_example.R            |   2 +-
 exec/marker_example.R             |   2 +-
 exec/pca_example.R                |   2 +-
 exec/scatterPlot_example.R        |   2 +-
 man/categoricalPalettes.Rd        |   2 +-
 man/colorPicker.Rd                |  21 ++-
 man/colorPicker2.Rd               |  35 ----
 man/colorPicker2UI.Rd             |  32 ----
 man/colorPickerUI.Rd              |  26 +--
 man/divergingPalettes.Rd          |   2 +-
 man/sequentialPalettes.Rd         |   2 +-
 25 files changed, 296 insertions(+), 448 deletions(-)
 delete mode 100644 R/colorPicker2.R
 delete mode 100644 exec/colorPicker2_example.R
 delete mode 100644 man/colorPicker2.Rd
 delete mode 100644 man/colorPicker2UI.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index e72ca3b..297c0d8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -42,7 +42,6 @@ Imports: shiny,
     FactoMineR,
     factoextra,
     heatmaply (>= 0.14.1),
-    shinyBS,
     shinythemes,
     shinycssloaders,
     log4r,
diff --git a/NAMESPACE b/NAMESPACE
index 32c24b5..fdd8ef2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -4,8 +4,6 @@ export(Clarion)
 export(and)
 export(andUI)
 export(colorPicker)
-export(colorPicker2)
-export(colorPicker2UI)
 export(colorPickerUI)
 export(columnSelector)
 export(columnSelectorUI)
diff --git a/R/colorPicker.R b/R/colorPicker.R
index 4e3b372..d4f103f 100644
--- a/R/colorPicker.R
+++ b/R/colorPicker.R
@@ -5,62 +5,258 @@
 #'
 #' @param id The ID of the modules namespace.
 #' @param label Either a character vector of length one with the label for the color scheme dropdown, or a character vector containing labels of the single colors.
-#' @param choices A character vector with choices for the color scheme dropdown. See \code{\link[shiny]{selectInput}}.
-#' @param selected.choice The initially selected value(s) of the dropdown. If NULL (default), the first value of schemes will be taken.
-#' @param show.reverse Logical, whether or not to show the reverse switch.
-#' @param show.transparency Logical, whether or not to show the transparency slider.
-#' @param single.colors Logical, whether or not to make a single color chooser. (Only if length(label) == 1 needed)
+#' @param custom Boolean if TRUE custom colors can be selected (Default = FALSE).
+#' @param multiple Boolean value, if set to TRUE custom colorpalettes can be made. Only if custom = TRUE (Default = FALSE).
+#' @param show.reverse Logical, whether or not to show the reverse switch (Default = TRUE).
+#' @param show.scaleoptions Logical, whether or not to show color scaling option winorize (Default = TRUE).
+#' @param show.transparency Logical, whether or not to show the transparency slider (Default = TRUE).
 #'
 #' @return A list with HTML tags from \code{\link[shiny]{tag}}.
 #'
-#' @section Single color mode:
-#' If one or more single colors can be chosen, the UI element names are prefix by \emph{color} followed by \code{make.names} ouput of \code{label}.
-#'
-#' @section To do:
-#' Replace ordinary textInput for single colors by a real colorPicker, e.g. from https://github.com/daattali/colourpicker
-#'
 #' @export
-colorPickerUI <- function(id, label = "Color scheme", choices = c("Blues", "Greens", "Greys", "Oranges", "Purples", "Reds"), selected.choice = NULL, show.reverse = TRUE, show.transparency = TRUE, single.colors = FALSE) {
+colorPickerUI <- function(id, label = "Color scheme", custom = FALSE, multiple = FALSE, show.reverse = TRUE, show.scaleoptions = TRUE, show.transparency = TRUE) {
   ns <- shiny::NS(id)
 
-  if(is.null(selected.choice)) {
-    selected.choice <- choices[[1]]
-  }
+  if(custom){
+    ret <- list(colourpicker::colourInput(ns("picker"), label = NULL, value = "red"))
 
-  if(length(label) == 1 & !single.colors) {
-    ret <- list(shiny::selectInput(ns("scheme"), label = label, choices = choices, selected = selected.choice))
+    if(multiple){
+      ret <- list(
+        shinyjs::useShinyjs(),
+        shiny::textInput(ns("palette"), label = NULL, value = "red,blue", placeholder = "e.g. black,#3c8dbc"),
+        ret,
+        shiny::actionButton(ns("add"), "add", style = "color: #fff; background-color: #3c8dbc"),
+        shiny::actionButton(ns("reset"), "reset", style = "color: #fff; background-color: #3c8dbc")
+      )
+    }
 
+    ret <- list(shiny::tags$b(label), ret)
+  }else{
+    ret <- list(shiny::tags$b(label), shiny::uiOutput(ns("palette")))
+  }
+
+  if(!custom | custom & multiple){
     if(show.reverse) {
       ret <- c(ret, list(shiny::checkboxInput(ns("reverse"), label = "Reverse scheme")))
     }
-  } else {
-    ret <- list()
-    for(name in make.names(label)) {
-      ret <- c(ret, list(colourpicker::colourInput(ns(paste0("color", name)), name, value = "red")))
+    if(show.scaleoptions) {
+      ret <- c(ret, limitUI(ns("winsorize"), label = "Winsorize to upper/lower"))
+    }
+    if(show.transparency) {
+      ret <- c(ret, list(shiny::sliderInput(ns("transparency"), label = "Transparency", min = 0, max = 1, value = 1)))
     }
   }
 
-  if(show.transparency) {
-    ret <- c(ret, list(shiny::sliderInput(ns("transparency"), label = "Transparency", min = 0, max = 1, value = 1)))
-  }
   shiny::tagList(ret)
 }
 
 #' colorPicker module server logic
 #'
-#' Provides server logic for the colorPicker module.
+#' Provides server logic for the colorPicker2 module.
 #'
 #' @param input Shiny's input object
 #' @param output Shiny's output object
 #' @param session Shiny's session object
+#' @param num.colors Define length of colorpalette vector (Default = 256).
+#' @param distribution Decide which palettes are selectable. One or more of list("sequential", "diverging", "categorical"). Defaults to "all" (Supports reactive).
+#' @param winsorize Numeric vector of two. Dynamicly change lower and upper limit (supports reactive). Defaults to NULL.
+#' @param selected Set the default selected palette.
 #'
-#' @return The \code{input} object.
+#' @details A custom colorpalette's return will be NULL if there is something wrong with it.
+#' @details equalize will be returned as FALSE if not selected.
 #'
-#' @section To do:
-#' Implement transparency calculation in case of one or more single colors.
+#' @return Reactive containing list(palette = c(colors), name = palette_name, transparency = Integer, reverse = Boolean, winsorize = NULL or a two-component vector containing lower and upper limits).
 #'
 #' @export
-colorPicker <- function(input, output, session) {
-  return(input)
+colorPicker <- function(input, output, session, num.colors = 256, distribution = "all", winsorize = NULL, selected = NULL) {
+  Sequential <- sequentialPalettes(num.colors)
+  Diverging <- divergingPalettes(num.colors)
+  Categorical <- categoricalPalettes(num.colors)
+
+  shinyjs::reset("reverse")
+  shinyjs::reset("transparency")
+
+  #handle reactive distribution
+  distribution.r <- shiny::reactive({
+    if(shiny::is.reactive(distribution)){
+      distribution()
+    }else{
+      distribution
+    }
+  })
+
+  if(!is.null(winsorize)) {
+    # handle reactive winsorize
+    winsorize.r <- shiny::reactive({
+      if(shiny::is.reactive(winsorize)) {
+        winsorize()
+      } else {
+        winsorize
+      }
+    })
+  }
+  limits <- shiny::callModule(limit, "winsorize", lower = if(!is.null(winsorize)){shiny::reactive(winsorize.r()[1])}, upper = if(!is.null(winsorize)){shiny::reactive(winsorize.r()[2])})
+
+  output$palette <- shiny::renderUI({
+    choices <- list()
+
+    if("sequential" %in% distribution.r()) choices <- append(choices, list(Sequential = names(Sequential)))
+    if("diverging" %in% distribution.r()) choices <- append(choices, list(Diverging = names(Diverging)))
+    if("categorical" %in% distribution.r()) choices <- append(choices, list(Categorical = names(Categorical)))
+    if(length(distribution.r()) == 1 && distribution.r() == "all") {
+      choices <- list(Sequential = names(Sequential), Diverging = names(Diverging), Categorical = names(Categorical))
+    }
+
+    shiny::selectInput(session$ns("palette"), label = NULL, choices = choices, selected = selected)
+  })
+
+  shiny::observeEvent(input$add, {
+    pal <- ifelse(input$palette == "", input$picker, paste(input$palette, input$picker, sep = ","))
+
+    shiny::updateTextInput(session, "palette", value = pal)
+  })
+
+  shiny::observeEvent(input$reset, {
+    shiny::updateTextInput(session, "palette", value = "")
+  })
+
+  #create custom colorpalette
+  custom <- shiny::reactive({
+    #returns TRUE if String is a valid color
+    isColor <- function(x){
+      res <- try(grDevices::col2rgb(x),silent=TRUE)
+      return(!"try-error"%in%class(res))
+    }
+
+    pal <- unlist(strsplit(input$palette, split = ",", fixed = TRUE))
+
+    if(length(pal) != 0){
+      valid <- unlist(lapply(pal, isColor))
+      if(!all(valid)){
+        shiny::showNotification(id = session$ns("notification"), shiny::HTML(paste("<b>ColorPicker</b><br/> Found invalid colors: ", paste(pal[!valid], collapse = ", "))), duration = NULL, type = "warning")
+        pal <- NULL
+      }else{
+        shiny::removeNotification(id = session$ns("notification"))
+        pal <- grDevices::colorRampPalette(pal)(num.colors)
+      }
+    }else{
+      shiny::showNotification(id = session$ns("notification"), shiny::HTML("<b>ColorPicker</b><br/> Warning no colors selected!"), duration = NULL, type = "warning")
+      pal <- NULL
+    }
+
+    return(pal)
+  })
+
+  output <- shiny::reactive({
+    if(is.null(input$palette)){
+      #custom single color
+      pal <- input$picker
+    }else{
+      #predefined palettes
+      if(is.null(shiny::isolate(input$picker))){
+        #get palette
+        if(input$palette %in% names(Sequential)){
+          pal <- Sequential[[input$palette]]
+        }else if(input$palette %in% names(Diverging)){
+          pal <- Diverging[[input$palette]]
+        }else {
+          pal <- Categorical[[input$palette]]
+        }
+      }else{
+        #custom palettes (multiple colors)
+        pal <- custom()
+      }
+      #reverse palette
+      if(!is.null(input$reverse)){
+        if(input$reverse){
+          pal <- rev(pal)
+        }
+      }
+    }
+
+    winsorize <- NULL
+    if(!is.null(limits())) {
+      winsorize <- c(limits()$lower, limits()$upper)
+    }
+
+    list(
+      palette = pal,
+      name = input$palette,
+      transparency = input$transparency,
+      reverse = input$reverse,
+      winsorize = winsorize
+    )
+  })
+
+  return(output)
+}
+
+#' Function to generate sequential (one-sided) color palettes (e.g. for expression, enrichment)
+#'
+#' @param n Number of colors to generate
+#'
+#' @return A data.table with (named) color palettes of length n
+#'
+sequentialPalettes <- function(n) {
+  Heat <- grDevices::colorRampPalette(rev(RColorBrewer::brewer.pal(9, "YlOrRd")))(n)
+  Viridis	<- viridis::viridis(n)
+  Magma <- viridis::magma(n)
+  Inferno	<- viridis::inferno(n)
+  Plasma <- viridis::plasma(n)
+  YlGnBu <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "YlGnBu"))(n)
+  Blues <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "Blues"))(n)
+  Reds <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "Reds"))(n)
+  Cubehelix	<- rje::cubeHelix(n)
+
+  BkOrYl <- grDevices::colorRampPalette(c("black", "orange", "yellow"))(n)						#one-sided (0 .. x): go enrichment
+  GnBu <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "GnBu"))(n)							#one-sided (0 .. x): expression
+  PuBuGn <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "PuBuGn"))(n)							#one-sided (0 .. x): expression
+  BuGnYlRd <- grDevices::colorRampPalette(c("#000041", "#0000CB", "#0081FF", "#02DA81", "#80FE1A", "#FDEE02", "#FFAB00", "#FF3300"))(n)	#one-sided (0 .. x): expression, ~=spectral
+
+  data.table::data.table(Heat, Viridis, Magma, Inferno, Plasma, YlGnBu, Blues, Reds, Cubehelix, BkOrYl, PuBuGn)
+}
+
+#' Function to generate diverging (two-sided) color palettes (e.g. for log2fc, zscore)
+#'
+#' @param n Number of colors to generate
+#'
+#' @return A data.table with (named) color palettes of length n
+#'
+divergingPalettes <- function(n) {
+  BuWtRd <- grDevices::colorRampPalette(c("royalblue4", "steelblue4", "white", "indianred", "firebrick4"))(n)
+  RdBkGr <- gplots::redgreen(n)
+  RdYlGr <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "RdYlGn"))(n)
+  YlWtPu <- grDevices::colorRampPalette(c("gold", "white", "white", "mediumpurple4"))(n)					#two-sided (-1 .. +1): correlation
+  Spectral <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "Spectral"))(n)
+
+  BuYlGn <- grDevices::colorRampPalette(c("dodgerblue4", "cadetblue1", "yellow", "darkolivegreen1", "darkgreen"))(n)	#two-sided (-x .. +x): fold-change
+  TqWtRd <- grDevices::colorRampPalette(c("darkslategray", "darkturquoise", "cornsilk", "indianred3", "red3"))(n)		#two-sided (-x .. +x): fold-change
+  YlGyRd <- grDevices::colorRampPalette(c("yellow", "grey25", "red"))(n)							#two-sided (-x .. +x): fold-change
+  RdBu <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "RdBu"))(n)							#two-sided (-x .. +x): fold-change
+  GnWtRd <- grDevices::colorRampPalette(c("chartreuse3", "white", "firebrick1"))(n)					#two-sided (-x .. +x): fold-change
+  RdYlBu <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "RdYlBu"))(n)							#two-sided (-x .. +x): fold-change
+  RdGy <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "RdGy"))(n)							#two-sided (-x .. +x): fold-change
+  PuOr <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "PuOr"))(n)							#two-sided (-x .. +x): fold-change
+
+  data.table::data.table(BuWtRd, Spectral, RdBkGr, YlWtPu, BuYlGn, GnWtRd, RdGy, PuOr)
+}
+
+#' Function to generate categorical (qualitative) color palettes
+#'
+#' @param n Number of colors to generate
+#'
+#' @return A data.table with (named) color palettes of length n
+#'
+categoricalPalettes <- function(n) {
+  Accent <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(8, "Accent"))(n)
+  Dark2 <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(8, "Dark2"))(n)
+  Paired <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(12, "Paired"))(n)
+  Pastel1 <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "Pastel1"))(n)
+  Pastel2 <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(8, "Pastel2"))(n)
+  Set1 <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "Set1"))(n)
+  Set2 <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(8, "Set2"))(n)
+  Set3 <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(12, "Set3"))(n)
+
+  data.table::data.table(Accent, Dark2, Paired, Pastel1, Pastel2, Set1, Set2, Set3)
 }
 
diff --git a/R/colorPicker2.R b/R/colorPicker2.R
deleted file mode 100644
index 48ba1f2..0000000
--- a/R/colorPicker2.R
+++ /dev/null
@@ -1,262 +0,0 @@
-#' colorPicker2 module UI representation
-#'
-#' The functions creates HTML tag definitions of its representation based on the parameters supplied.
-#' Currently, two UI can be created for the user to choose either (a) colors from a given color scheme, or (b) choose one or more single colors.
-#'
-#' @param id The ID of the modules namespace.
-#' @param label Either a character vector of length one with the label for the color scheme dropdown, or a character vector containing labels of the single colors.
-#' @param custom Boolean if TRUE custom colors can be selected (Default = FALSE).
-#' @param multiple Boolean value, if set to TRUE custom colorpalettes can be made. Only if custom = TRUE (Default = FALSE).
-#' @param show.reverse Logical, whether or not to show the reverse switch (Default = TRUE).
-#' @param show.scaleoptions Logical, whether or not to show color scaling option winorize (Default = TRUE).
-#' @param show.transparency Logical, whether or not to show the transparency slider (Default = TRUE).
-#'
-#' @return A list with HTML tags from \code{\link[shiny]{tag}}.
-#'
-#' @export
-colorPicker2UI <- function(id, label = "Color scheme", custom = FALSE, multiple = FALSE, show.reverse = TRUE, show.scaleoptions = TRUE, show.transparency = TRUE) {
-  ns <- shiny::NS(id)
-
-  if(custom){
-    ret <- list(colourpicker::colourInput(ns("picker"), label = NULL, value = "red"))
-
-    if(multiple){
-      ret <- list(
-        shinyjs::useShinyjs(),
-        shinyBS::tipify(shiny::textInput(ns("palette"), label = NULL, value = "red,blue", placeholder = "e.g. black,#3c8dbc"), title = "Comma delimited colors (hex or name)", placement = "right"),
-        ret,
-        shiny::actionButton(ns("add"), "add", style = "color: #fff; background-color: #3c8dbc"),
-        shiny::actionButton(ns("reset"), "reset", style = "color: #fff; background-color: #3c8dbc")
-      )
-    }
-
-    ret <- list(shiny::tags$b(label), ret)
-  }else{
-    ret <- list(shiny::tags$b(label), shiny::uiOutput(ns("palette")))
-  }
-
-  if(!custom | custom & multiple){
-    if(show.reverse) {
-      ret <- c(ret, list(shiny::checkboxInput(ns("reverse"), label = "Reverse scheme")))
-    }
-    if(show.scaleoptions) {
-      ret <- c(ret, limitUI(ns("winsorize"), label = "Winsorize to upper/lower"))
-    }
-    if(show.transparency) {
-      ret <- c(ret, list(shiny::sliderInput(ns("transparency"), label = "Transparency", min = 0, max = 1, value = 1)))
-    }
-  }
-
-  shiny::tagList(ret)
-}
-
-#' colorPicker2 module server logic
-#'
-#' Provides server logic for the colorPicker2 module.
-#'
-#' @param input Shiny's input object
-#' @param output Shiny's output object
-#' @param session Shiny's session object
-#' @param num.colors Define length of colorpalette vector (Default = 256).
-#' @param distribution Decide which palettes are selectable. One or more of list("sequential", "diverging", "categorical"). Defaults to "all" (Supports reactive).
-#' @param winsorize Numeric vector of two. Dynamicly change lower and upper limit (supports reactive). Defaults to NULL.
-#' @param selected Set the default selected palette.
-#'
-#' @details A custom colorpalette's return will be NULL if there is something wrong with it.
-#' @details equalize will be returned as FALSE if not selected.
-#'
-#' @return Reactive containing list(palette = c(colors), name = palette_name, transparency = Integer, reverse = Boolean, winsorize = NULL or a two-component vector containing lower and upper limits).
-#'
-#' @export
-colorPicker2 <- function(input, output, session, num.colors = 256, distribution = "all", winsorize = NULL, selected = NULL) {
-  Sequential <- sequentialPalettes(num.colors)
-  Diverging <- divergingPalettes(num.colors)
-  Categorical <- categoricalPalettes(num.colors)
-
-  shinyjs::reset("reverse")
-  shinyjs::reset("transparency")
-
-  #handle reactive distribution
-  distribution.r <- shiny::reactive({
-    if(shiny::is.reactive(distribution)){
-      distribution()
-    }else{
-      distribution
-    }
-  })
-
-  if(!is.null(winsorize)) {
-    # handle reactive winsorize
-    winsorize.r <- shiny::reactive({
-      if(shiny::is.reactive(winsorize)) {
-        winsorize()
-      } else {
-        winsorize
-      }
-    })
-  }
-  limits <- shiny::callModule(limit, "winsorize", lower = if(!is.null(winsorize)){shiny::reactive(winsorize.r()[1])}, upper = if(!is.null(winsorize)){shiny::reactive(winsorize.r()[2])})
-
-  output$palette <- shiny::renderUI({
-    choices <- list()
-
-    if("sequential" %in% distribution.r()) choices <- append(choices, list(Sequential = names(Sequential)))
-    if("diverging" %in% distribution.r()) choices <- append(choices, list(Diverging = names(Diverging)))
-    if("categorical" %in% distribution.r()) choices <- append(choices, list(Categorical = names(Categorical)))
-    if(length(distribution.r()) == 1 && distribution.r() == "all") {
-      choices <- list(Sequential = names(Sequential), Diverging = names(Diverging), Categorical = names(Categorical))
-    }
-
-    shiny::selectInput(session$ns("palette"), label = NULL, choices = choices, selected = selected)
-  })
-
-  shiny::observeEvent(input$add, {
-    pal <- ifelse(input$palette == "", input$picker, paste(input$palette, input$picker, sep = ","))
-
-    shiny::updateTextInput(session, "palette", value = pal)
-  })
-
-  shiny::observeEvent(input$reset, {
-    shiny::updateTextInput(session, "palette", value = "")
-  })
-
-  #create custom colorpalette
-  custom <- shiny::reactive({
-    #returns TRUE if String is a valid color
-    isColor <- function(x){
-      res <- try(grDevices::col2rgb(x),silent=TRUE)
-      return(!"try-error"%in%class(res))
-    }
-
-    pal <- unlist(strsplit(input$palette, split = ",", fixed = TRUE))
-
-    if(length(pal) != 0){
-      valid <- unlist(lapply(pal, isColor))
-      if(!all(valid)){
-        shiny::showNotification(id = session$ns("notification"), shiny::HTML(paste("<b>ColorPicker</b><br/> Found invalid colors: ", paste(pal[!valid], collapse = ", "))), duration = NULL, type = "warning")
-        pal <- NULL
-      }else{
-        shiny::removeNotification(id = session$ns("notification"))
-        pal <- grDevices::colorRampPalette(pal)(num.colors)
-      }
-    }else{
-      shiny::showNotification(id = session$ns("notification"), shiny::HTML("<b>ColorPicker</b><br/> Warning no colors selected!"), duration = NULL, type = "warning")
-      pal <- NULL
-    }
-
-    return(pal)
-  })
-
-  output <- shiny::reactive({
-    if(is.null(input$palette)){
-      #custom single color
-      pal <- input$picker
-    }else{
-      #predefined palettes
-      if(is.null(shiny::isolate(input$picker))){
-        #get palette
-        if(input$palette %in% names(Sequential)){
-          pal <- Sequential[[input$palette]]
-        }else if(input$palette %in% names(Diverging)){
-          pal <- Diverging[[input$palette]]
-        }else {
-          pal <- Categorical[[input$palette]]
-        }
-      }else{
-        #custom palettes (multiple colors)
-        pal <- custom()
-      }
-      #reverse palette
-      if(!is.null(input$reverse)){
-        if(input$reverse){
-          pal <- rev(pal)
-        }
-      }
-    }
-
-    winsorize <- NULL
-    if(!is.null(limits())) {
-      winsorize <- c(limits()$lower, limits()$upper)
-    }
-
-    list(
-      palette = pal,
-      name = input$palette,
-      transparency = input$transparency,
-      reverse = input$reverse,
-      winsorize = winsorize
-    )
-  })
-
-  return(output)
-}
-
-#' Function to generate sequential (one-sided) color palettes (e.g. for expression, enrichment)
-#'
-#' @param n Number of colors to generate
-#'
-#' @return A data.table with (named) color palettes of length n
-#'
-sequentialPalettes <- function(n) {
-  Heat <- grDevices::colorRampPalette(rev(RColorBrewer::brewer.pal(9, "YlOrRd")))(n)
-  Viridis	<- viridis::viridis(n)
-  Magma <- viridis::magma(n)
-  Inferno	<- viridis::inferno(n)
-  Plasma <- viridis::plasma(n)
-  YlGnBu <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "YlGnBu"))(n)
-  Blues <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "Blues"))(n)
-  Reds <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "Reds"))(n)
-  Cubehelix	<- rje::cubeHelix(n)
-
-  BkOrYl <- grDevices::colorRampPalette(c("black", "orange", "yellow"))(n)						#one-sided (0 .. x): go enrichment
-  GnBu <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "GnBu"))(n)							#one-sided (0 .. x): expression
-  PuBuGn <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "PuBuGn"))(n)							#one-sided (0 .. x): expression
-  BuGnYlRd <- grDevices::colorRampPalette(c("#000041", "#0000CB", "#0081FF", "#02DA81", "#80FE1A", "#FDEE02", "#FFAB00", "#FF3300"))(n)	#one-sided (0 .. x): expression, ~=spectral
-
-  data.table::data.table(Heat, Viridis, Magma, Inferno, Plasma, YlGnBu, Blues, Reds, Cubehelix, BkOrYl, PuBuGn)
-}
-
-#' Function to generate diverging (two-sided) color palettes (e.g. for log2fc, zscore)
-#'
-#' @param n Number of colors to generate
-#'
-#' @return A data.table with (named) color palettes of length n
-#'
-divergingPalettes <- function(n) {
-  BuWtRd <- grDevices::colorRampPalette(c("royalblue4", "steelblue4", "white", "indianred", "firebrick4"))(n)
-  RdBkGr <- gplots::redgreen(n)
-  RdYlGr <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "RdYlGn"))(n)
-  YlWtPu <- grDevices::colorRampPalette(c("gold", "white", "white", "mediumpurple4"))(n)					#two-sided (-1 .. +1): correlation
-  Spectral <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "Spectral"))(n)
-
-  BuYlGn <- grDevices::colorRampPalette(c("dodgerblue4", "cadetblue1", "yellow", "darkolivegreen1", "darkgreen"))(n)	#two-sided (-x .. +x): fold-change
-  TqWtRd <- grDevices::colorRampPalette(c("darkslategray", "darkturquoise", "cornsilk", "indianred3", "red3"))(n)		#two-sided (-x .. +x): fold-change
-  YlGyRd <- grDevices::colorRampPalette(c("yellow", "grey25", "red"))(n)							#two-sided (-x .. +x): fold-change
-  RdBu <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "RdBu"))(n)							#two-sided (-x .. +x): fold-change
-  GnWtRd <- grDevices::colorRampPalette(c("chartreuse3", "white", "firebrick1"))(n)					#two-sided (-x .. +x): fold-change
-  RdYlBu <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "RdYlBu"))(n)							#two-sided (-x .. +x): fold-change
-  RdGy <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "RdGy"))(n)							#two-sided (-x .. +x): fold-change
-  PuOr <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "PuOr"))(n)							#two-sided (-x .. +x): fold-change
-
-  data.table::data.table(BuWtRd, Spectral, RdBkGr, YlWtPu, BuYlGn, GnWtRd, RdGy, PuOr)
-}
-
-#' Function to generate categorical (qualitative) color palettes
-#'
-#' @param n Number of colors to generate
-#'
-#' @return A data.table with (named) color palettes of length n
-#'
-categoricalPalettes <- function(n) {
-  Accent <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(8, "Accent"))(n)
-  Dark2 <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(8, "Dark2"))(n)
-  Paired <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(12, "Paired"))(n)
-  Pastel1 <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "Pastel1"))(n)
-  Pastel2 <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(8, "Pastel2"))(n)
-  Set1 <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "Set1"))(n)
-  Set2 <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(8, "Set2"))(n)
-  Set3 <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(12, "Set3"))(n)
-
-  data.table::data.table(Accent, Dark2, Paired, Pastel1, Pastel2, Set1, Set2, Set3)
-}
-
diff --git a/R/geneView.R b/R/geneView.R
index 16ff9b3..29be373 100644
--- a/R/geneView.R
+++ b/R/geneView.R
@@ -56,7 +56,7 @@ geneViewUI <- function(id, plot.columns = 3){
             shiny::column(
               width = 3,
               shiny::div(id = ns("guide_color"),
-                         colorPicker2UI(id = ns("color"), show.transparency = FALSE, show.scaleoptions = FALSE)),
+                         colorPickerUI(id = ns("color"), show.transparency = FALSE, show.scaleoptions = FALSE)),
               shiny::div(id = ns("guide_plotColumns"),
                          shiny::sliderInput(ns("plotColumns"), label = "Plot Columns", min = 1, max = 7, value = plot.columns, step = 1))
             )
@@ -142,7 +142,7 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
   })
 
   # modules/ ui #####
-  colorPicker <- shiny::callModule(colorPicker2, "color", distribution = "all", selected = "Dark2")
+  colorPicker <- shiny::callModule(colorPicker, "color", distribution = "all", selected = "Dark2")
   transform <- shiny::callModule(transformation, "transform", shiny::reactive(as.matrix(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes), selector$selectedColumns(), with = FALSE])))
   selector <- shiny::callModule(columnSelector, "selector", type.columns = shiny::reactive(object()$metadata[level != "feature", c("key", "level")]), columnTypeLabel = "Select Columns")
   custom_label <- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes)]), sep = label.sep)
@@ -181,7 +181,7 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
     shinyjs::reset("plotType")
     shinyjs::reset("groupby")
     shinyjs::reset("plotColumns")
-    colorPicker <<- shiny::callModule(colorPicker2, "color", distribution = "all", selected = "Dark2")
+    colorPicker <<- shiny::callModule(colorPicker, "color", distribution = "all", selected = "Dark2")
     transform <<- shiny::callModule(transformation, "transform", shiny::reactive(as.matrix(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes), selector$selectedColumns(), with = FALSE])))
     selector <<- shiny::callModule(columnSelector, "selector", type.columns = shiny::reactive(object()$metadata[level != "feature", c("key", "level")]), columnTypeLabel = "Select Columns")
     custom_label <<- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes)]), sep = label.sep)
diff --git a/R/global_cor_heatmap.R b/R/global_cor_heatmap.R
index b97bbf7..dc1dda4 100644
--- a/R/global_cor_heatmap.R
+++ b/R/global_cor_heatmap.R
@@ -81,7 +81,7 @@ global_cor_heatmapUI <- function(id) {
                   choices = c("Sequential", "Diverging"),
                   multiple = FALSE
                 ),
-                colorPicker2UI(
+                colorPickerUI(
                   id = ns("color"),
                   show.transparency = FALSE
                 )
@@ -208,7 +208,7 @@ global_cor_heatmap <- function(input, output, session, clarion, plot.method = "s
   # load internal modules
   columns <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
   transform <- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selectedColumns(), with = FALSE])))
-  colorPicker <- shiny::callModule(colorPicker2, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(result_data()[, -1])))
+  colorPicker <- shiny::callModule(colorPicker, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(result_data()[, -1])))
 
   # load dynamic ui
   if (plot.method == "static") {
@@ -236,7 +236,7 @@ global_cor_heatmap <- function(input, output, session, clarion, plot.method = "s
     shinyjs::reset("column_label")
     columns <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
     transform <<- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selectedColumns(), with = FALSE])))
-    colorPicker <<- shiny::callModule(colorPicker2, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(result_data()[, -1])))
+    colorPicker <<- shiny::callModule(colorPicker, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(result_data()[, -1])))
     clearPlot(TRUE)
   })
 
diff --git a/R/heatmap.R b/R/heatmap.R
index e685e0a..84ba2c2 100644
--- a/R/heatmap.R
+++ b/R/heatmap.R
@@ -57,7 +57,7 @@ heatmapUI <- function(id, row.label = TRUE) {
                          choices = c("Sequential", "Diverging"),
                          multiple = FALSE
                        ),
-                       colorPicker2UI(ns("color"), show.transparency = FALSE)
+                       colorPickerUI(ns("color"), show.transparency = FALSE)
             )
           ),
           shiny::column(
@@ -156,7 +156,7 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
   # modules/ ui #####
   columns <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
   transform <- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selectedColumns(), with = FALSE])))
-  colorPicker <- shiny::callModule(colorPicker2, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(transform$data())))
+  colorPicker <- shiny::callModule(colorPicker, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(transform$data())))
   custom_label <- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data), label = "Select row label", sep = label.sep, disable = shiny::reactive(!input$row.label))
 
   # automatic unitlabel
@@ -178,7 +178,7 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
     shinyjs::reset("column.label")
     columns <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
     transform <<- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selectedColumns(), with = FALSE])))
-    colorPicker <<- shiny::callModule(colorPicker2, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(transform$data())))
+    colorPicker <<- shiny::callModule(colorPicker, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(transform$data())))
     custom_label <<- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data), label = "Select row label", sep = label.sep, disable = shiny::reactive(!input$row.label))
     clearPlot(TRUE)
   })
diff --git a/R/marker.R b/R/marker.R
index e068dff..511f7f2 100644
--- a/R/marker.R
+++ b/R/marker.R
@@ -11,7 +11,7 @@ markerUI <- function(id, label = "Highlight/ Label Selected Features"){
 
   shiny::tagList(
     shiny::selectInput(ns("highlight"), label = label, choices = c("Disabled", "Highlight", "Exclusive")),
-    colorPicker2UI(ns("color"), label = "Color", custom = TRUE),
+    colorPickerUI(ns("color"), label = "Color", custom = TRUE),
     labelUI(ns("label"))
 
   )
@@ -43,7 +43,7 @@ marker <- function(input, output, session, clarion){
   })
 
   # modules #####
-  color <- shiny::callModule(colorPicker2, "color")
+  color <- shiny::callModule(colorPicker, "color")
   labeller <-  shiny::callModule(label, "label", data = shiny::reactive(object()$data), unique = FALSE)
 
   return(
diff --git a/R/pca.R b/R/pca.R
index 2f776ee..9ac43f4 100644
--- a/R/pca.R
+++ b/R/pca.R
@@ -48,7 +48,7 @@ pcaUI <- function(id, show.label = TRUE) {
                        shiny::sliderInput(ns("labelsize"), label = "Label size", min = 1, max = 20, value = 5, round = TRUE)
             ),
             shiny::div(id = ns("guide_color"),
-                       colorPicker2UI(id = ns("colorPicker"), show.scaleoptions = FALSE, show.transparency = FALSE)
+                       colorPickerUI(id = ns("colorPicker"), show.scaleoptions = FALSE, show.transparency = FALSE)
             )
           )
         ),
@@ -136,7 +136,7 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
   columnSelect <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
   factor_data <- shiny::callModule(label, "group", label = "Select color grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columnSelect$selectedColumns(), !"key"]), unique = FALSE)
   factor_data2 <- shiny::callModule(label, "group2", label = "Select shape grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columnSelect$selectedColumns(), !"key"]), unique = FALSE)
-  colorPicker <- shiny::callModule(colorPicker2, "colorPicker",  distribution = "categorical", selected = "Dark2")
+  colorPicker <- shiny::callModule(colorPicker, "colorPicker",  distribution = "categorical", selected = "Dark2")
 
   # update dimension inputs
   shiny::observe({
@@ -164,7 +164,7 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
     columnSelect <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
     factor_data <<- shiny::callModule(label, "group", label = "Select color grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columnSelect$selectedColumns(), !"key"]), unique = FALSE)
     factor_data2 <<- shiny::callModule(label, "group2", label = "Select shape grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columnSelect$selectedColumns(), !"key"]), unique = FALSE)
-    colorPicker <<- shiny::callModule(colorPicker2, "colorPicker",  distribution = "categorical", selected = "Dark2")
+    colorPicker <<- shiny::callModule(colorPicker, "colorPicker",  distribution = "categorical", selected = "Dark2")
     clearPlot(TRUE)
   })
 
diff --git a/R/scatterPlot.R b/R/scatterPlot.R
index 2ae8830..99e1da8 100644
--- a/R/scatterPlot.R
+++ b/R/scatterPlot.R
@@ -71,7 +71,7 @@ scatterPlotUI <- function(id) {
           shiny::column(
             width = 3,
             shiny::div(id = ns("guide_color"),
-                       colorPicker2UI(id = ns("color"))
+                       colorPickerUI(id = ns("color"))
             ),
             shiny::div(id = ns("guide_pointsize"),
                        shiny::sliderInput(
@@ -186,7 +186,7 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
   xaxis <- shiny::callModule(columnSelector, "xaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_x$method()))
   yaxis <- shiny::callModule(columnSelector, "yaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_y$method()))
   zaxis <- shiny::callModule(columnSelector, "zaxis", type.columns = shiny::reactive(object()$metadata[, intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", labelLabel = "Color label", multiple = FALSE, none = TRUE)
-  colorPicker <- shiny::callModule(colorPicker2, "color", distribution = "all", winsorize = shiny::reactive(switch(shiny::isTruthy(zaxis$selectedColumn()) + 1, NULL, equalize(object()$data[, zaxis$selectedColumn(), with = FALSE]))))
+  colorPicker <- shiny::callModule(colorPicker, "color", distribution = "all", winsorize = shiny::reactive(switch(shiny::isTruthy(zaxis$selectedColumn()) + 1, NULL, equalize(object()$data[, zaxis$selectedColumn(), with = FALSE]))))
   transform_x <- shiny::callModule(transformation, "transform_x", data = shiny::reactive(as.matrix(object()$data[, xaxis$selectedColumn(), with = FALSE])))
   transform_y <- shiny::callModule(transformation, "transform_y", data = shiny::reactive(as.matrix(object()$data[, yaxis$selectedColumn(), with = FALSE])))
   # transform highlight data
@@ -222,7 +222,7 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
     xaxis <<- shiny::callModule(columnSelector, "xaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_x$method()))
     yaxis <<- shiny::callModule(columnSelector, "yaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_y$method()))
     zaxis <<- shiny::callModule(columnSelector, "zaxis", type.columns = shiny::reactive(object()$metadata[, intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", multiple = FALSE, none = TRUE)
-    colorPicker <<- shiny::callModule(colorPicker2, "color", distribution = "all", winsorize = shiny::reactive(switch(shiny::isTruthy(zaxis$selectedColumn()) + 1, NULL, equalize(object()$data[, zaxis$selectedColumn(), with = FALSE]))))
+    colorPicker <<- shiny::callModule(colorPicker, "color", distribution = "all", winsorize = shiny::reactive(switch(shiny::isTruthy(zaxis$selectedColumn()) + 1, NULL, equalize(object()$data[, zaxis$selectedColumn(), with = FALSE]))))
     transform_x <<- shiny::callModule(transformation, "transform_x", data = shiny::reactive(as.matrix(object()$data[, xaxis$selectedColumn(), with = FALSE])))
     transform_y <<- shiny::callModule(transformation, "transform_y", data = shiny::reactive(as.matrix(object()$data[, yaxis$selectedColumn(), with = FALSE])))
     # transform highlight data
diff --git a/exec/colorPicker2_example.R b/exec/colorPicker2_example.R
deleted file mode 100644
index 04c2721..0000000
--- a/exec/colorPicker2_example.R
+++ /dev/null
@@ -1,33 +0,0 @@
-library(shiny)
-source("../R/colorPicker2.R")
-
-
-ui <- fluidPage(
-  column(width = 4,
-         colorPicker2UI("custom.single", custom = TRUE, label = "Single color select"),
-         verbatimTextOutput("cs.t")
-         ),
-  column(width = 4,
-         colorPicker2UI("custom.multiple", custom = TRUE, multiple = TRUE, label = "Multiple color select/ custom colorpalette"),
-         verbatimTextOutput("cm.t")
-         ),
-  column(width = 4,
-         colorPicker2UI("defined", label = "predefined palettes", show.scaleoptions = T),
-         verbatimTextOutput("d.t")
-         )
-  )
-
-
-server <- function(input, output) {
-  def <- callModule(colorPicker2, "defined", distribution = "all", num.color = 3)
-  cs <- callModule(colorPicker2, "custom.single", num.colors = 3)
-  cm <- callModule(colorPicker2, "custom.multiple", num.colors = 3)
-
-  output$d.t <- renderPrint(def())
-  output$cs.t <- renderPrint(cs())
-  output$cm.t <- renderPrint(cm())
-
-}
-
-# Run the application
-shinyApp(ui = ui, server = server)
diff --git a/exec/colorPicker_example.R b/exec/colorPicker_example.R
index 8c70c85..38c889b 100644
--- a/exec/colorPicker_example.R
+++ b/exec/colorPicker_example.R
@@ -2,12 +2,30 @@ library(shiny)
 source("../R/colorPicker.R")
 
 
-ui <- fluidPage(colorPickerUI("id"))
+ui <- fluidPage(
+  column(width = 4,
+         colorPickerUI("custom.single", custom = TRUE, label = "Single color select"),
+         verbatimTextOutput("cs.t")
+         ),
+  column(width = 4,
+         colorPickerUI("custom.multiple", custom = TRUE, multiple = TRUE, label = "Multiple color select/ custom colorpalette"),
+         verbatimTextOutput("cm.t")
+         ),
+  column(width = 4,
+         colorPickerUI("defined", label = "predefined palettes", show.scaleoptions = T),
+         verbatimTextOutput("d.t")
+         )
+  )
+
 
 server <- function(input, output) {
-  mod <- callModule(colorPicker, "id")
+  def <- callModule(colorPicker, "defined", distribution = "all", num.color = 3)
+  cs <- callModule(colorPicker, "custom.single", num.colors = 3)
+  cm <- callModule(colorPicker, "custom.multiple", num.colors = 3)
 
-  observe(print(mod$scheme))
+  output$d.t <- renderPrint(def())
+  output$cs.t <- renderPrint(cs())
+  output$cm.t <- renderPrint(cm())
 
 }
 
diff --git a/exec/geneView_example.R b/exec/geneView_example.R
index 5a17273..592bd2f 100644
--- a/exec/geneView_example.R
+++ b/exec/geneView_example.R
@@ -2,7 +2,7 @@
 library(shiny)
 library(shinydashboard)
 source("../R/function.R")
-source("../R/colorPicker2.R")
+source("../R/colorPicker.R")
 source("../R/transformation.R")
 source("../R/geneView.R")
 source("../R/columnSelector.R")
diff --git a/exec/global_cor_heatmap_example.R b/exec/global_cor_heatmap_example.R
index 9a43f15..78fa5be 100644
--- a/exec/global_cor_heatmap_example.R
+++ b/exec/global_cor_heatmap_example.R
@@ -1,7 +1,7 @@
 library(shiny)
 library(shinydashboard)
 source("../R/function.R")
-source("../R/colorPicker2.R")
+source("../R/colorPicker.R")
 source("../R/columnSelector.R")
 source("../R/transformation.R")
 source("../R/global_cor_heatmap.R")
diff --git a/exec/heatmap_example.R b/exec/heatmap_example.R
index e15d6fe..9e0bd23 100644
--- a/exec/heatmap_example.R
+++ b/exec/heatmap_example.R
@@ -1,7 +1,7 @@
 library(shiny)
 library(shinydashboard)
 source("../R/function.R")
-source("../R/colorPicker2.R")
+source("../R/colorPicker.R")
 source("../R/columnSelector.R")
 source("../R/transformation.R")
 source("../R/heatmap.R")
diff --git a/exec/marker_example.R b/exec/marker_example.R
index 8baf245..e990de3 100644
--- a/exec/marker_example.R
+++ b/exec/marker_example.R
@@ -1,7 +1,7 @@
 
 library(shiny)
 source("../R/marker.R")
-source("../R/colorPicker2.R")
+source("../R/colorPicker.R")
 source("../R/label.R")
 source("../R/limit.R")
 source("../R/clarion.R")
diff --git a/exec/pca_example.R b/exec/pca_example.R
index 90a5bb9..4ea4570 100644
--- a/exec/pca_example.R
+++ b/exec/pca_example.R
@@ -7,7 +7,7 @@ source("../R/pca.R")
 source("../R/global.R")
 source("../R/clarion.R")
 source("../R/label.R")
-source("../R/colorPicker2.R")
+source("../R/colorPicker.R")
 source("../R/limit.R")
 
 ####Test Data
diff --git a/exec/scatterPlot_example.R b/exec/scatterPlot_example.R
index 7a16840..df336c6 100644
--- a/exec/scatterPlot_example.R
+++ b/exec/scatterPlot_example.R
@@ -2,7 +2,7 @@
 library(shiny)
 library(shinydashboard)
 source("../R/function.R")
-source("../R/colorPicker2.R")
+source("../R/colorPicker.R")
 source("../R/columnSelector.R")
 source("../R/transformation.R")
 source("../R/scatterPlot.R")
diff --git a/man/categoricalPalettes.Rd b/man/categoricalPalettes.Rd
index da8e4f0..fbc0a82 100644
--- a/man/categoricalPalettes.Rd
+++ b/man/categoricalPalettes.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/colorPicker2.R
+% Please edit documentation in R/colorPicker.R
 \name{categoricalPalettes}
 \alias{categoricalPalettes}
 \title{Function to generate categorical (qualitative) color palettes}
diff --git a/man/colorPicker.Rd b/man/colorPicker.Rd
index 515c07c..8e73328 100644
--- a/man/colorPicker.Rd
+++ b/man/colorPicker.Rd
@@ -4,7 +4,8 @@
 \alias{colorPicker}
 \title{colorPicker module server logic}
 \usage{
-colorPicker(input, output, session)
+colorPicker(input, output, session, num.colors = 256, distribution = "all",
+  winsorize = NULL, selected = NULL)
 }
 \arguments{
 \item{input}{Shiny's input object}
@@ -12,15 +13,23 @@ colorPicker(input, output, session)
 \item{output}{Shiny's output object}
 
 \item{session}{Shiny's session object}
+
+\item{num.colors}{Define length of colorpalette vector (Default = 256).}
+
+\item{distribution}{Decide which palettes are selectable. One or more of list("sequential", "diverging", "categorical"). Defaults to "all" (Supports reactive).}
+
+\item{winsorize}{Numeric vector of two. Dynamicly change lower and upper limit (supports reactive). Defaults to NULL.}
+
+\item{selected}{Set the default selected palette.}
 }
 \value{
-The \code{input} object.
+Reactive containing list(palette = c(colors), name = palette_name, transparency = Integer, reverse = Boolean, winsorize = NULL or a two-component vector containing lower and upper limits).
 }
 \description{
-Provides server logic for the colorPicker module.
+Provides server logic for the colorPicker2 module.
 }
-\section{To do}{
+\details{
+A custom colorpalette's return will be NULL if there is something wrong with it.
 
-Implement transparency calculation in case of one or more single colors.
+equalize will be returned as FALSE if not selected.
 }
-
diff --git a/man/colorPicker2.Rd b/man/colorPicker2.Rd
deleted file mode 100644
index 0d87a9d..0000000
--- a/man/colorPicker2.Rd
+++ /dev/null
@@ -1,35 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/colorPicker2.R
-\name{colorPicker2}
-\alias{colorPicker2}
-\title{colorPicker2 module server logic}
-\usage{
-colorPicker2(input, output, session, num.colors = 256, distribution = "all",
-  winsorize = NULL, selected = NULL)
-}
-\arguments{
-\item{input}{Shiny's input object}
-
-\item{output}{Shiny's output object}
-
-\item{session}{Shiny's session object}
-
-\item{num.colors}{Define length of colorpalette vector (Default = 256).}
-
-\item{distribution}{Decide which palettes are selectable. One or more of list("sequential", "diverging", "categorical"). Defaults to "all" (Supports reactive).}
-
-\item{winsorize}{Numeric vector of two. Dynamicly change lower and upper limit (supports reactive). Defaults to NULL.}
-
-\item{selected}{Set the default selected palette.}
-}
-\value{
-Reactive containing list(palette = c(colors), name = palette_name, transparency = Integer, reverse = Boolean, winsorize = NULL or a two-component vector containing lower and upper limits).
-}
-\description{
-Provides server logic for the colorPicker2 module.
-}
-\details{
-A custom colorpalette's return will be NULL if there is something wrong with it.
-
-equalize will be returned as FALSE if not selected.
-}
diff --git a/man/colorPicker2UI.Rd b/man/colorPicker2UI.Rd
deleted file mode 100644
index 576b2d3..0000000
--- a/man/colorPicker2UI.Rd
+++ /dev/null
@@ -1,32 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/colorPicker2.R
-\name{colorPicker2UI}
-\alias{colorPicker2UI}
-\title{colorPicker2 module UI representation}
-\usage{
-colorPicker2UI(id, label = "Color scheme", custom = FALSE,
-  multiple = FALSE, show.reverse = TRUE, show.scaleoptions = TRUE,
-  show.transparency = TRUE)
-}
-\arguments{
-\item{id}{The ID of the modules namespace.}
-
-\item{label}{Either a character vector of length one with the label for the color scheme dropdown, or a character vector containing labels of the single colors.}
-
-\item{custom}{Boolean if TRUE custom colors can be selected (Default = FALSE).}
-
-\item{multiple}{Boolean value, if set to TRUE custom colorpalettes can be made. Only if custom = TRUE (Default = FALSE).}
-
-\item{show.reverse}{Logical, whether or not to show the reverse switch (Default = TRUE).}
-
-\item{show.scaleoptions}{Logical, whether or not to show color scaling option winorize (Default = TRUE).}
-
-\item{show.transparency}{Logical, whether or not to show the transparency slider (Default = TRUE).}
-}
-\value{
-A list with HTML tags from \code{\link[shiny]{tag}}.
-}
-\description{
-The functions creates HTML tag definitions of its representation based on the parameters supplied.
-Currently, two UI can be created for the user to choose either (a) colors from a given color scheme, or (b) choose one or more single colors.
-}
diff --git a/man/colorPickerUI.Rd b/man/colorPickerUI.Rd
index 13db175..5f8113c 100644
--- a/man/colorPickerUI.Rd
+++ b/man/colorPickerUI.Rd
@@ -4,24 +4,24 @@
 \alias{colorPickerUI}
 \title{colorPicker module UI representation}
 \usage{
-colorPickerUI(id, label = "Color scheme", choices = c("Blues", "Greens",
-  "Greys", "Oranges", "Purples", "Reds"), selected.choice = NULL,
-  show.reverse = TRUE, show.transparency = TRUE, single.colors = FALSE)
+colorPickerUI(id, label = "Color scheme", custom = FALSE,
+  multiple = FALSE, show.reverse = TRUE, show.scaleoptions = TRUE,
+  show.transparency = TRUE)
 }
 \arguments{
 \item{id}{The ID of the modules namespace.}
 
 \item{label}{Either a character vector of length one with the label for the color scheme dropdown, or a character vector containing labels of the single colors.}
 
-\item{choices}{A character vector with choices for the color scheme dropdown. See \code{\link[shiny]{selectInput}}.}
+\item{custom}{Boolean if TRUE custom colors can be selected (Default = FALSE).}
 
-\item{selected.choice}{The initially selected value(s) of the dropdown. If NULL (default), the first value of schemes will be taken.}
+\item{multiple}{Boolean value, if set to TRUE custom colorpalettes can be made. Only if custom = TRUE (Default = FALSE).}
 
-\item{show.reverse}{Logical, whether or not to show the reverse switch.}
+\item{show.reverse}{Logical, whether or not to show the reverse switch (Default = TRUE).}
 
-\item{show.transparency}{Logical, whether or not to show the transparency slider.}
+\item{show.scaleoptions}{Logical, whether or not to show color scaling option winorize (Default = TRUE).}
 
-\item{single.colors}{Logical, whether or not to make a single color chooser. (Only if length(label) == 1 needed)}
+\item{show.transparency}{Logical, whether or not to show the transparency slider (Default = TRUE).}
 }
 \value{
 A list with HTML tags from \code{\link[shiny]{tag}}.
@@ -30,13 +30,3 @@ A list with HTML tags from \code{\link[shiny]{tag}}.
 The functions creates HTML tag definitions of its representation based on the parameters supplied.
 Currently, two UI can be created for the user to choose either (a) colors from a given color scheme, or (b) choose one or more single colors.
 }
-\section{Single color mode}{
-
-If one or more single colors can be chosen, the UI element names are prefix by \emph{color} followed by \code{make.names} ouput of \code{label}.
-}
-
-\section{To do}{
-
-Replace ordinary textInput for single colors by a real colorPicker, e.g. from https://github.com/daattali/colourpicker
-}
-
diff --git a/man/divergingPalettes.Rd b/man/divergingPalettes.Rd
index 8513548..d8d6211 100644
--- a/man/divergingPalettes.Rd
+++ b/man/divergingPalettes.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/colorPicker2.R
+% Please edit documentation in R/colorPicker.R
 \name{divergingPalettes}
 \alias{divergingPalettes}
 \title{Function to generate diverging (two-sided) color palettes (e.g. for log2fc, zscore)}
diff --git a/man/sequentialPalettes.Rd b/man/sequentialPalettes.Rd
index 3ac8f99..b22d2dd 100644
--- a/man/sequentialPalettes.Rd
+++ b/man/sequentialPalettes.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/colorPicker2.R
+% Please edit documentation in R/colorPicker.R
 \name{sequentialPalettes}
 \alias{sequentialPalettes}
 \title{Function to generate sequential (one-sided) color palettes (e.g. for expression, enrichment)}

From 1caf9e8859e26bddcf0b453c06ea50b5e8efbe38 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 20 Jun 2018 09:29:37 +0200
Subject: [PATCH 34/75] bump package version to v2.0.0

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 297c0d8..f1a85a1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: wilson
 Type: Package
 Title: WIlsON Webbased Interactive Omics visualizatioN
-Version: 1.0.0
+Version: 2.0.0
 Authors@R: c(
     person("Hendrik", "Schultheis", email = "hendrik.schultheis@mpi-bn.mpg.de", role = c("aut", "cre")),
     person("Jens", "Preussner", email = "jens.preussner@mpi-bn.mpg.de", role = "aut"),

From b73286c0ee1e15abdca4c06749339fa617e49052 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 21 Jun 2018 10:10:03 +0200
Subject: [PATCH 35/75] clarion$is_delimited: fixed wrong return

---
 R/clarion.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/clarion.R b/R/clarion.R
index 5d0d990..1483e7f 100644
--- a/R/clarion.R
+++ b/R/clarion.R
@@ -73,7 +73,7 @@ Clarion <- R6::R6Class("Clarion",
                          },
                          is_delimited = function(x) {
                            if (is.element("type", names(self$metadata))) {
-                             return(self$metadata[key == x] == "array")
+                             return(self$metadata[key == x, type] == "array")
                            } else {
                              return(FALSE)
                            }

From 0eb9c60946f87ad7ff0d764b55ade18c5d278f05 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 21 Jun 2018 10:17:47 +0200
Subject: [PATCH 36/75] featureSelector: updated docu

---
 R/featureSelector.R    | 2 +-
 man/featureSelector.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/featureSelector.R b/R/featureSelector.R
index ea73398..2b2be56 100644
--- a/R/featureSelector.R
+++ b/R/featureSelector.R
@@ -60,7 +60,7 @@ featureSelectorUI <- function(id){
 #' @param truncate Truncate datatable entries at x characters (Default = 30).
 #' @param selection.default Decide whether everything or nothing is selected on default (no filters applied). Either "all" or "none" (Default = "all").
 #'
-#' @details Keep in mind that the order of features is the order in which delimiter, multiple, contains, ranged and step are evaluated.
+#' @details Keep in mind that the order of features (columns in clarion$data) is the order in which multiple, contains, ranged and step are evaluated.
 #'
 #' @return Reactive containing names list: Selected data as reactive containing clarion object (object). Used filter to select data (filter).
 #'
diff --git a/man/featureSelector.Rd b/man/featureSelector.Rd
index 3a53695..6499180 100644
--- a/man/featureSelector.Rd
+++ b/man/featureSelector.Rd
@@ -36,5 +36,5 @@ Reactive containing names list: Selected data as reactive containing clarion obj
 featureSelector module server logic
 }
 \details{
-Keep in mind that the order of features is the order in which delimiter, multiple, contains, ranged and step are evaluated.
+Keep in mind that the order of features (columns in clarion$data) is the order in which multiple, contains, ranged and step are evaluated.
 }

From 7f26cc4ba0425ad5ba35b5e64c14943beebf0d10 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 21 Jun 2018 10:36:24 +0200
Subject: [PATCH 37/75] geneView: changed guide

---
 R/geneView.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/geneView.R b/R/geneView.R
index 29be373..6c8f5e0 100644
--- a/R/geneView.R
+++ b/R/geneView.R
@@ -423,7 +423,7 @@ geneViewGuide <- function(session) {
       Select one or more columns to be used as a label instead of the names above.",
     "guide_columnSelection" = "<h4>Column selection</h4>
       First select a column type for visualization, then select individual columns from all columns of the chosen type.<br/>
-      Second select grouping factor(s). 'None' will result in no grouping, multiple selection in a single merged factor.<br/>
+      Second select grouping factor(s). Condense the above selected columns to factor(s). 'None' will result in no grouping, multiple selection in a single merged factor.<br/>
       After that choose a factor by which the given subset is grouped. E.g. 'condition' will generate a plot for each condition or uses the conditions as x-axis ticks, based on the choosen plot type.",
     "guide_type" = "<h4>Plot type</h4>
       Choose the preferred type of plot that will be rendered.",

From ce951d317d5f66332a8ce73c7019e7a8b7a7fb0a Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 21 Jun 2018 15:09:20 +0200
Subject: [PATCH 38/75] featureSelector: fixed filter crash on data column not
 defined in metadata

---
 R/featureSelector.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/featureSelector.R b/R/featureSelector.R
index 2b2be56..71425e9 100644
--- a/R/featureSelector.R
+++ b/R/featureSelector.R
@@ -83,7 +83,7 @@ featureSelector <- function(input, output, session, clarion, multiple = TRUE, co
   # delimiter vector
   # only delimit type = array
   delimiter <- shiny::reactive({
-    sapply(names(object()$data), function(x) {
+    sapply(object()$metadata[["key"]], function(x) {
       if (object()$is_delimited(x)) {
         return(object()$get_delimiter())
       } else {

From 7db391a5e7b52d70bf6f5a22b9023c22e9618191 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 21 Jun 2018 15:55:44 +0200
Subject: [PATCH 39/75] clarion: omit not defined columns from data

---
 R/clarion.R    | 16 ++++++++++------
 man/Clarion.Rd |  4 ++--
 2 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/R/clarion.R b/R/clarion.R
index 1483e7f..ada66a0 100644
--- a/R/clarion.R
+++ b/R/clarion.R
@@ -20,8 +20,8 @@
 #'     \item{\code{get_factors()}}{
 #'       Returns a data.table columns: key and factor(s) if any. Named factors (e.g. factor1="name") will be cropped to their name.
 #'     }
-#'     \item{\code{validate()}}{
-#'       Check the object for inconsistencies.
+#'     \item{\code{validate(solve = TRUE)}}{
+#'       Check the object for inconsistencies. For solve = TRUE try to resolve some warnings.
 #'     }
 #'   }
 #'
@@ -97,7 +97,7 @@ Clarion <- R6::R6Class("Clarion",
 
                            return(factor_table)
                          },
-                         validate = function() {
+                         validate = function(solve = TRUE) {
                            # validate header
                            private$check_delimiter()
                            # validate metadata
@@ -107,7 +107,7 @@ Clarion <- R6::R6Class("Clarion",
                            private$check_type()
                            private$check_label()
                            # validate data
-                           private$check_dataHeader()
+                           private$check_dataHeader(solve)
                            private$check_dataMin()
                            private$check_dataColumnTypes()
                          },
@@ -216,11 +216,15 @@ Clarion <- R6::R6Class("Clarion",
                            }
                          },
                          ## data checks
-                         check_dataHeader = function() {
+                         check_dataHeader = function(solve = TRUE) {
                            # case: column not defined in metadata
                            missing <- setdiff(names(self$data), self$metadata[["key"]])
                            if (length(missing) > 0) {
-                             warning("Metadata rows and data columns differ! Following rows are missing in metadata: ", paste0(missing, collapse = ", "))
+                             if (solve) {
+                               # omit undefined columns
+                               self$data[, (missing) := NULL]
+                             }
+                             warning("Metadata rows and data columns differ! Following rows are missing in metadata: ", paste0(missing, collapse = ", "), if (solve) "\nOmitting data column(s)!")
                            }
                            # case: duplicated column names
                            if (anyDuplicated(names(self$data))) {
diff --git a/man/Clarion.Rd b/man/Clarion.Rd
index 9b4e4fa..8c0f4aa 100644
--- a/man/Clarion.Rd
+++ b/man/Clarion.Rd
@@ -45,8 +45,8 @@ This object is used by all top-level wilson modules.
     \item{\code{get_factors()}}{
       Returns a data.table columns: key and factor(s) if any. Named factors (e.g. factor1="name") will be cropped to their name.
     }
-    \item{\code{validate()}}{
-      Check the object for inconsistencies.
+    \item{\code{validate(solve = TRUE)}}{
+      Check the object for inconsistencies. For solve = TRUE try to resolve some warnings.
     }
   }
 }

From 67bb1827280990a0c09e0a579443f0b7c27c6f72 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Mon, 25 Jun 2018 13:25:01 +0200
Subject: [PATCH 40/75] fixed notes (win-builder): package name in title,
 software not in '', spelling errors

---
 DESCRIPTION | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f1a85a1..e040e15 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,13 +1,13 @@
 Package: wilson
 Type: Package
-Title: WIlsON Webbased Interactive Omics visualizatioN
+Title: Web-based Interactive Omics visualizatioN
 Version: 2.0.0
 Authors@R: c(
     person("Hendrik", "Schultheis", email = "hendrik.schultheis@mpi-bn.mpg.de", role = c("aut", "cre")),
     person("Jens", "Preussner", email = "jens.preussner@mpi-bn.mpg.de", role = "aut"),
     person("Looso", "Mario", email = "mario.looso@mpi-bn.mpg.de", role = "aut"))
-Description: This package provides modules for webbased tools that use plot based strategies to visualize and analyze multi-omics data.
-    WIlsON utilizes the Rshiny and Plotly frameworks to provide a user friendly dashboard for interactive plotting.
+Description: This package provides modules for web-based tools that use plot based strategies to visualize and analyze multi-omics data.
+    'wilson' utilizes the 'shiny' and 'plotly' frameworks to provide a user friendly dashboard for interactive plotting.
 URL: https://github.molgen.mpg.de/loosolab/wilson
 BugReports: https://github.molgen.mpg.de/loosolab/wilson/issues
 License: MIT + file LICENSE

From 915080a8651051e7808209a061848067026764a6 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Mon, 25 Jun 2018 13:42:57 +0200
Subject: [PATCH 41/75] fixed spelling errors

---
 R/colorPicker.R        | 4 ++--
 R/columnSelector.R     | 4 ++--
 R/function.R           | 6 +++---
 R/geneView.R           | 2 +-
 R/heatmap.R            | 2 +-
 R/label.R              | 4 ++--
 R/parser.R             | 2 +-
 man/colorPicker.Rd     | 2 +-
 man/colorPickerUI.Rd   | 2 +-
 man/columnSelector.Rd  | 4 ++--
 man/create_geneview.Rd | 2 +-
 man/create_pca.Rd      | 2 +-
 man/download.Rd        | 2 +-
 man/geneView.Rd        | 2 +-
 man/heatmap.Rd         | 2 +-
 man/label.Rd           | 4 ++--
 man/parse_MaxQuant.Rd  | 2 +-
 17 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/R/colorPicker.R b/R/colorPicker.R
index d4f103f..6297397 100644
--- a/R/colorPicker.R
+++ b/R/colorPicker.R
@@ -8,7 +8,7 @@
 #' @param custom Boolean if TRUE custom colors can be selected (Default = FALSE).
 #' @param multiple Boolean value, if set to TRUE custom colorpalettes can be made. Only if custom = TRUE (Default = FALSE).
 #' @param show.reverse Logical, whether or not to show the reverse switch (Default = TRUE).
-#' @param show.scaleoptions Logical, whether or not to show color scaling option winorize (Default = TRUE).
+#' @param show.scaleoptions Logical, whether or not to show color scaling option winsorize (Default = TRUE).
 #' @param show.transparency Logical, whether or not to show the transparency slider (Default = TRUE).
 #'
 #' @return A list with HTML tags from \code{\link[shiny]{tag}}.
@@ -59,7 +59,7 @@ colorPickerUI <- function(id, label = "Color scheme", custom = FALSE, multiple =
 #' @param session Shiny's session object
 #' @param num.colors Define length of colorpalette vector (Default = 256).
 #' @param distribution Decide which palettes are selectable. One or more of list("sequential", "diverging", "categorical"). Defaults to "all" (Supports reactive).
-#' @param winsorize Numeric vector of two. Dynamicly change lower and upper limit (supports reactive). Defaults to NULL.
+#' @param winsorize Numeric vector of two. Dynamically change lower and upper limit (supports reactive). Defaults to NULL.
 #' @param selected Set the default selected palette.
 #'
 #' @details A custom colorpalette's return will be NULL if there is something wrong with it.
diff --git a/R/columnSelector.R b/R/columnSelector.R
index bfd3f99..0c5c299 100644
--- a/R/columnSelector.R
+++ b/R/columnSelector.R
@@ -35,8 +35,8 @@ columnSelectorUI <- function(id, label = F, title = NULL) {
 #' @param labelLabel Change label above label text input.
 #' @param multiple Boolean value whether multiple values can be selected in second selector. (Default = TRUE)
 #' @param none If TRUE adds "None to secondSelector and select is. (Default = FALSE)
-#' @param sep Used to seperate labels on multi value selection.
-#' @param suffix Added to label only on multiple = FALSE (supports reactive). Also uses sep as seperator.
+#' @param sep Used to separate labels on multi value selection.
+#' @param suffix Added to label only on multiple = FALSE (supports reactive). Also uses sep as separator.
 #'
 #' @return Returns the input. As named list: names("type", "selectedColumns", "label")
 #'
diff --git a/R/function.R b/R/function.R
index 8e82ba7..7cfbcd4 100644
--- a/R/function.R
+++ b/R/function.R
@@ -305,7 +305,7 @@ create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL,
 #' @param shapes Vector of shapes see \code{\link[graphics]{points}}. Will recycle/ cut off shapes if needed. Default = c(15:25)
 #' @param dimensionA Number of dimension displayed on X-Axis.
 #' @param dimensionB Number of dimension displayed on Y-Axis.
-#' @param dimensions Number of dimesions to create.
+#' @param dimensions Number of dimensions to create.
 #' @param on.columns Boolean perform pca on columns or rows.
 #' @param labels Boolean show labels.
 #' @param custom.labels Vector of custom labels. Will replace columnnames.
@@ -753,7 +753,7 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
 #' @param grouping data.table metadata containing:
 #'                                                column1 : key
 #'                                                column2 : factor1
-#' @param plot.type String specifing which plot type is used c("box", "line", "violin", "bar").
+#' @param plot.type String specifying which plot type is used c("box", "line", "violin", "bar").
 #' @param facet.target Target to plot on x-Axis c("gene", "condition").
 #' @param facet.cols Number of plots per row.
 #' @param colors Vector of colors used for color palette
@@ -1199,7 +1199,7 @@ searchData <- function(input, choices, options = c("=", "<", ">"), min. = min(ch
 #' @param height in centimeter.
 #' @param ppi pixel per inch. Defaults to 72.
 #' @param save_plot Logical if plot object should be saved as .RData.
-#' @param ui List of user inputs. Will be converted to Javascript Object Notation. See \code{\link[RJSONIO]{toJSON}}
+#' @param ui List of user inputs. Will be converted to JavaScript Object Notation. See \code{\link[RJSONIO]{toJSON}}
 #'
 #' @return See \code{\link[utils]{zip}}.
 download <- function(file, filename, plot, width, height, ppi = 72, save_plot = TRUE, ui = NULL) {
diff --git a/R/geneView.R b/R/geneView.R
index 6c8f5e0..d8f391b 100644
--- a/R/geneView.R
+++ b/R/geneView.R
@@ -86,7 +86,7 @@ geneViewUI <- function(id, plot.columns = 3){
 #' @param session Shiny's session object.
 #' @param clarion A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)
 #' @param plot.method Choose which method is used for plotting. Either "static" or "interactive" (Default = "static").
-#' @param label.sep Seperator used for label merging (Default = ", ").
+#' @param label.sep Separator used for label merging (Default = ", ").
 #' @param width Width of the plot in cm. Defaults to minimal size for readable labels and supports reactive.
 #' @param height Height of the plot in cm. Defaults to minimal size for readable labels and supports reactive.
 #' @param ppi Pixel per inch. Defaults to 72 and supports reactive.
diff --git a/R/heatmap.R b/R/heatmap.R
index 84ba2c2..c6b4759 100644
--- a/R/heatmap.R
+++ b/R/heatmap.R
@@ -93,7 +93,7 @@ heatmapUI <- function(id, row.label = TRUE) {
 #' @param session Shiny's session object
 #' @param clarion A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)
 #' @param plot.method Choose which method is used for plotting. Either "static" or "interactive" (Default = "static").
-#' @param label.sep Seperator used for label merging (Default = ", ").
+#' @param label.sep Separator used for label merging (Default = ", ").
 #' @param width Width of the plot in cm. Defaults to minimal size for readable labels and supports reactive.
 #' @param height Height of the plot in cm. Defaults to minimal size for readable labels and supports reactive.
 #' @param ppi Pixel per inch. Defaults to 72 and supports reactive.
diff --git a/R/label.R b/R/label.R
index 64817e3..ea3e0b1 100644
--- a/R/label.R
+++ b/R/label.R
@@ -21,9 +21,9 @@ labelUI <- function(id){
 #' @param data Data.table used for label creation. Column names will be used for selection. (supports reactive)
 #' @param label Set label of selectizeInput.
 #' @param multiple Allow multiple selection which will be merged with sep (default = TRUE).
-#' @param sep Seperator used to collapse selection (default = ", ").
+#' @param sep Separator used to collapse selection (default = ", ").
 #' @param unique Make labels unique. Defaults to TRUE. See \code{\link[base]{make.unique}}.
-#' @param unique_sep Seperator used for unique (default = "_"). Should differ from sep.
+#' @param unique_sep Separator used for unique (default = "_"). Should differ from sep.
 #' @param disable Reactive containing boolean. To disable/ enable module.
 #'
 #' @return Reactive containing list(label = vector of strings or NULL on empty selection, selected = user input).
diff --git a/R/parser.R b/R/parser.R
index da86729..7df2e6c 100644
--- a/R/parser.R
+++ b/R/parser.R
@@ -11,7 +11,7 @@
 #'       Intensity 'experiment_name'
 #' Do you want both add "Intensity" to the list.
 #' Do you only want the sample add "Intensity;exp" to the list
-#' Anything else like 'Intensity;ex' or 'Intesity;' results in writing both.
+#' Anything else like 'Intensity;ex' or 'Intensity;' results in writing both.
 #' Only works if there are samples of that type. If not, column does not show up in file
 #'
 #' @author Rene Wiegandt
diff --git a/man/colorPicker.Rd b/man/colorPicker.Rd
index 8e73328..5581d4d 100644
--- a/man/colorPicker.Rd
+++ b/man/colorPicker.Rd
@@ -18,7 +18,7 @@ colorPicker(input, output, session, num.colors = 256, distribution = "all",
 
 \item{distribution}{Decide which palettes are selectable. One or more of list("sequential", "diverging", "categorical"). Defaults to "all" (Supports reactive).}
 
-\item{winsorize}{Numeric vector of two. Dynamicly change lower and upper limit (supports reactive). Defaults to NULL.}
+\item{winsorize}{Numeric vector of two. Dynamically change lower and upper limit (supports reactive). Defaults to NULL.}
 
 \item{selected}{Set the default selected palette.}
 }
diff --git a/man/colorPickerUI.Rd b/man/colorPickerUI.Rd
index 5f8113c..2c2260a 100644
--- a/man/colorPickerUI.Rd
+++ b/man/colorPickerUI.Rd
@@ -19,7 +19,7 @@ colorPickerUI(id, label = "Color scheme", custom = FALSE,
 
 \item{show.reverse}{Logical, whether or not to show the reverse switch (Default = TRUE).}
 
-\item{show.scaleoptions}{Logical, whether or not to show color scaling option winorize (Default = TRUE).}
+\item{show.scaleoptions}{Logical, whether or not to show color scaling option winsorize (Default = TRUE).}
 
 \item{show.transparency}{Logical, whether or not to show the transparency slider (Default = TRUE).}
 }
diff --git a/man/columnSelector.Rd b/man/columnSelector.Rd
index 8f785aa..6cb7593 100644
--- a/man/columnSelector.Rd
+++ b/man/columnSelector.Rd
@@ -31,9 +31,9 @@ sub_label = optional, added to id/ label}
 
 \item{none}{If TRUE adds "None to secondSelector and select is. (Default = FALSE)}
 
-\item{sep}{Used to seperate labels on multi value selection.}
+\item{sep}{Used to separate labels on multi value selection.}
 
-\item{suffix}{Added to label only on multiple = FALSE (supports reactive). Also uses sep as seperator.}
+\item{suffix}{Added to label only on multiple = FALSE (supports reactive). Also uses sep as separator.}
 }
 \value{
 Returns the input. As named list: names("type", "selectedColumns", "label")
diff --git a/man/create_geneview.Rd b/man/create_geneview.Rd
index 8ca3d08..c4f7932 100644
--- a/man/create_geneview.Rd
+++ b/man/create_geneview.Rd
@@ -16,7 +16,7 @@ create_geneview(data, grouping, plot.type = "line", facet.target = "gene",
 column1 : key
 column2 : factor1}
 
-\item{plot.type}{String specifing which plot type is used c("box", "line", "violin", "bar").}
+\item{plot.type}{String specifying which plot type is used c("box", "line", "violin", "bar").}
 
 \item{facet.target}{Target to plot on x-Axis c("gene", "condition").}
 
diff --git a/man/create_pca.Rd b/man/create_pca.Rd
index 74b7f83..a0da5f8 100644
--- a/man/create_pca.Rd
+++ b/man/create_pca.Rd
@@ -29,7 +29,7 @@ create_pca(data, color.group = NULL, color.title = NULL, palette = NULL,
 
 \item{dimensionB}{Number of dimension displayed on Y-Axis.}
 
-\item{dimensions}{Number of dimesions to create.}
+\item{dimensions}{Number of dimensions to create.}
 
 \item{on.columns}{Boolean perform pca on columns or rows.}
 
diff --git a/man/download.Rd b/man/download.Rd
index d210e9f..ba92f84 100644
--- a/man/download.Rd
+++ b/man/download.Rd
@@ -24,7 +24,7 @@ download(file, filename, plot, width, height, ppi = 72, save_plot = TRUE,
 
 \item{save_plot}{Logical if plot object should be saved as .RData.}
 
-\item{ui}{List of user inputs. Will be converted to Javascript Object Notation. See \code{\link[RJSONIO]{toJSON}}}
+\item{ui}{List of user inputs. Will be converted to JavaScript Object Notation. See \code{\link[RJSONIO]{toJSON}}}
 }
 \value{
 See \code{\link[utils]{zip}}.
diff --git a/man/geneView.Rd b/man/geneView.Rd
index a9852c2..882f0ce 100644
--- a/man/geneView.Rd
+++ b/man/geneView.Rd
@@ -19,7 +19,7 @@ geneView(input, output, session, clarion, plot.method = "static",
 
 \item{plot.method}{Choose which method is used for plotting. Either "static" or "interactive" (Default = "static").}
 
-\item{label.sep}{Seperator used for label merging (Default = ", ").}
+\item{label.sep}{Separator used for label merging (Default = ", ").}
 
 \item{width}{Width of the plot in cm. Defaults to minimal size for readable labels and supports reactive.}
 
diff --git a/man/heatmap.Rd b/man/heatmap.Rd
index a54c357..e26c853 100644
--- a/man/heatmap.Rd
+++ b/man/heatmap.Rd
@@ -19,7 +19,7 @@ heatmap(input, output, session, clarion, plot.method = "static",
 
 \item{plot.method}{Choose which method is used for plotting. Either "static" or "interactive" (Default = "static").}
 
-\item{label.sep}{Seperator used for label merging (Default = ", ").}
+\item{label.sep}{Separator used for label merging (Default = ", ").}
 
 \item{width}{Width of the plot in cm. Defaults to minimal size for readable labels and supports reactive.}
 
diff --git a/man/label.Rd b/man/label.Rd
index 45da611..6db0f24 100644
--- a/man/label.Rd
+++ b/man/label.Rd
@@ -21,11 +21,11 @@ label(input, output, session, data, label = "Select label columns",
 
 \item{multiple}{Allow multiple selection which will be merged with sep (default = TRUE).}
 
-\item{sep}{Seperator used to collapse selection (default = ", ").}
+\item{sep}{Separator used to collapse selection (default = ", ").}
 
 \item{unique}{Make labels unique. Defaults to TRUE. See \code{\link[base]{make.unique}}.}
 
-\item{unique_sep}{Seperator used for unique (default = "_"). Should differ from sep.}
+\item{unique_sep}{Separator used for unique (default = "_"). Should differ from sep.}
 
 \item{disable}{Reactive containing boolean. To disable/ enable module.}
 }
diff --git a/man/parse_MaxQuant.Rd b/man/parse_MaxQuant.Rd
index 364d969..300c565 100644
--- a/man/parse_MaxQuant.Rd
+++ b/man/parse_MaxQuant.Rd
@@ -38,7 +38,7 @@ For example:
       Intensity 'experiment_name'
 Do you want both add "Intensity" to the list.
 Do you only want the sample add "Intensity;exp" to the list
-Anything else like 'Intensity;ex' or 'Intesity;' results in writing both.
+Anything else like 'Intensity;ex' or 'Intensity;' results in writing both.
 Only works if there are samples of that type. If not, column does not show up in file
 }
 \author{

From 84f492eeea90a805c6ee01a9d1b5a60bbce40831 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 27 Jun 2018 10:27:34 +0200
Subject: [PATCH 42/75] removed shinybs

---
 .buildkite/wilson-env.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.buildkite/wilson-env.yml b/.buildkite/wilson-env.yml
index 32b23f0..574754e 100644
--- a/.buildkite/wilson-env.yml
+++ b/.buildkite/wilson-env.yml
@@ -43,4 +43,3 @@ dependencies:
   - r-devtools
   - "readline==6.3"
   - r-roxygen2
-  - r-shinybs

From 7422194d1c942a62147eca84a621091816e0e46d Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 27 Jun 2018 13:57:12 +0200
Subject: [PATCH 43/75] add reverse dependency checks

---
 .Rbuildignore      |   1 +
 revdep/README.md   |  58 +++++++++++++++++++++++++++++++++++++++++++++
 revdep/checks.rds  | Bin 0 -> 938 bytes
 revdep/data.sqlite | Bin 0 -> 20480 bytes
 revdep/problems.md |  58 +++++++++++++++++++++++++++++++++++++++++++++
 revdep/timing.md   |   5 ++++
 6 files changed, 122 insertions(+)
 create mode 100644 revdep/README.md
 create mode 100644 revdep/checks.rds
 create mode 100644 revdep/data.sqlite
 create mode 100644 revdep/problems.md
 create mode 100644 revdep/timing.md

diff --git a/.Rbuildignore b/.Rbuildignore
index 4d88d31..d73b159 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,3 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.buildkite.*
+^revdep$
diff --git a/revdep/README.md b/revdep/README.md
new file mode 100644
index 0000000..e8c8c48
--- /dev/null
+++ b/revdep/README.md
@@ -0,0 +1,58 @@
+# Setup
+
+## Platform
+
+|setting  |value                        |
+|:--------|:----------------------------|
+|version  |R version 3.5.0 (2018-04-23) |
+|system   |x86_64, mingw32              |
+|ui       |RStudio (1.2.747)            |
+|language |(EN)                         |
+|collate  |German_Germany.1252          |
+|tz       |Europe/Berlin                |
+|date     |2018-06-27                   |
+
+## Packages
+
+|package         |*  |version |date       |source                              |
+|:---------------|:--|:-------|:----------|:-----------------------------------|
+|circlize        |   |0.4.4   |2018-06-10 |CRAN (R 3.5.0)                      |
+|colourpicker    |   |1.0     |2017-09-27 |CRAN (R 3.5.0)                      |
+|ComplexHeatmap  |   |1.18.1  |2018-06-19 |Bioconductor (R 3.5.0)              |
+|data.table      |   |1.11.4  |2018-05-27 |CRAN (R 3.5.0)                      |
+|DESeq2          |   |1.20.0  |2018-05-01 |Bioconductor                        |
+|DT              |   |0.4     |2018-01-30 |CRAN (R 3.5.0)                      |
+|factoextra      |   |1.0.5   |2017-08-22 |CRAN (R 3.5.0)                      |
+|FactoMineR      |   |1.41    |2018-05-04 |CRAN (R 3.5.0)                      |
+|ggplot2         |   |2.2.1   |2016-12-30 |CRAN (R 3.5.0)                      |
+|ggrepel         |   |0.8.0   |2018-05-09 |CRAN (R 3.5.0)                      |
+|gplots          |   |3.0.1   |2016-03-30 |CRAN (R 3.5.0)                      |
+|heatmaply       |   |0.15.0  |2018-06-23 |CRAN (R 3.5.0)                      |
+|log4r           |   |0.2     |2014-09-29 |CRAN (R 3.5.0)                      |
+|openssl         |   |1.0.1   |2018-03-03 |CRAN (R 3.5.0)                      |
+|plotly          |   |4.7.1   |2017-07-29 |CRAN (R 3.5.0)                      |
+|plyr            |   |1.8.4   |2016-06-08 |CRAN (R 3.5.0)                      |
+|R6              |   |2.2.2   |2017-06-17 |CRAN (R 3.5.0)                      |
+|RColorBrewer    |   |1.1-2   |2014-12-07 |CRAN (R 3.5.0)                      |
+|reshape         |   |0.8.7   |2017-08-06 |CRAN (R 3.5.0)                      |
+|rintrojs        |   |0.2.0   |2017-07-04 |CRAN (R 3.5.0)                      |
+|rje             |   |1.9     |2014-08-06 |CRAN (R 3.5.0)                      |
+|rjson           |   |0.2.20  |2018-06-08 |CRAN (R 3.5.0)                      |
+|RJSONIO         |   |1.3-0   |2014-07-28 |CRAN (R 3.5.0)                      |
+|scales          |   |0.5.0   |2017-08-24 |CRAN (R 3.5.0)                      |
+|shiny           |   |1.1.0   |2018-05-17 |CRAN (R 3.5.0)                      |
+|shinycssloaders |   |0.2.0   |2017-05-12 |CRAN (R 3.5.0)                      |
+|shinydashboard  |   |0.7.0   |2018-03-21 |CRAN (R 3.5.0)                      |
+|shinyjs         |   |1.0     |2018-01-08 |CRAN (R 3.5.0)                      |
+|shinythemes     |   |1.1.1   |2016-10-12 |CRAN (R 3.5.0)                      |
+|viridis         |   |0.5.1   |2018-03-29 |CRAN (R 3.5.0)                      |
+|webshot         |   |0.5.0   |2017-11-29 |CRAN (R 3.5.0)                      |
+|wilson          |   |2.0.0   |2018-06-27 |local (HendrikSchultheis/wilson@NA) |
+
+# Check results
+
+0 packages
+
+
+
+
diff --git a/revdep/checks.rds b/revdep/checks.rds
new file mode 100644
index 0000000000000000000000000000000000000000..f1e582f2d9de6aa7e14363812d8bb8bb11f68b50
GIT binary patch
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diff --git a/revdep/problems.md b/revdep/problems.md
new file mode 100644
index 0000000..0204215
--- /dev/null
+++ b/revdep/problems.md
@@ -0,0 +1,58 @@
+# Setup
+
+## Platform
+
+|setting  |value                        |
+|:--------|:----------------------------|
+|version  |R version 3.5.0 (2018-04-23) |
+|system   |x86_64, mingw32              |
+|ui       |RStudio (1.2.747)            |
+|language |(EN)                         |
+|collate  |German_Germany.1252          |
+|tz       |Europe/Berlin                |
+|date     |2018-06-27                   |
+
+## Packages
+
+|package         |*  |version |date       |source                              |
+|:---------------|:--|:-------|:----------|:-----------------------------------|
+|circlize        |   |0.4.4   |2018-06-10 |CRAN (R 3.5.0)                      |
+|colourpicker    |   |1.0     |2017-09-27 |CRAN (R 3.5.0)                      |
+|ComplexHeatmap  |   |1.18.1  |2018-06-19 |Bioconductor (R 3.5.0)              |
+|data.table      |   |1.11.4  |2018-05-27 |CRAN (R 3.5.0)                      |
+|DESeq2          |   |1.20.0  |2018-05-01 |Bioconductor                        |
+|DT              |   |0.4     |2018-01-30 |CRAN (R 3.5.0)                      |
+|factoextra      |   |1.0.5   |2017-08-22 |CRAN (R 3.5.0)                      |
+|FactoMineR      |   |1.41    |2018-05-04 |CRAN (R 3.5.0)                      |
+|ggplot2         |   |2.2.1   |2016-12-30 |CRAN (R 3.5.0)                      |
+|ggrepel         |   |0.8.0   |2018-05-09 |CRAN (R 3.5.0)                      |
+|gplots          |   |3.0.1   |2016-03-30 |CRAN (R 3.5.0)                      |
+|heatmaply       |   |0.15.0  |2018-06-23 |CRAN (R 3.5.0)                      |
+|log4r           |   |0.2     |2014-09-29 |CRAN (R 3.5.0)                      |
+|openssl         |   |1.0.1   |2018-03-03 |CRAN (R 3.5.0)                      |
+|plotly          |   |4.7.1   |2017-07-29 |CRAN (R 3.5.0)                      |
+|plyr            |   |1.8.4   |2016-06-08 |CRAN (R 3.5.0)                      |
+|R6              |   |2.2.2   |2017-06-17 |CRAN (R 3.5.0)                      |
+|RColorBrewer    |   |1.1-2   |2014-12-07 |CRAN (R 3.5.0)                      |
+|reshape         |   |0.8.7   |2017-08-06 |CRAN (R 3.5.0)                      |
+|rintrojs        |   |0.2.0   |2017-07-04 |CRAN (R 3.5.0)                      |
+|rje             |   |1.9     |2014-08-06 |CRAN (R 3.5.0)                      |
+|rjson           |   |0.2.20  |2018-06-08 |CRAN (R 3.5.0)                      |
+|RJSONIO         |   |1.3-0   |2014-07-28 |CRAN (R 3.5.0)                      |
+|scales          |   |0.5.0   |2017-08-24 |CRAN (R 3.5.0)                      |
+|shiny           |   |1.1.0   |2018-05-17 |CRAN (R 3.5.0)                      |
+|shinycssloaders |   |0.2.0   |2017-05-12 |CRAN (R 3.5.0)                      |
+|shinydashboard  |   |0.7.0   |2018-03-21 |CRAN (R 3.5.0)                      |
+|shinyjs         |   |1.0     |2018-01-08 |CRAN (R 3.5.0)                      |
+|shinythemes     |   |1.1.1   |2016-10-12 |CRAN (R 3.5.0)                      |
+|viridis         |   |0.5.1   |2018-03-29 |CRAN (R 3.5.0)                      |
+|webshot         |   |0.5.0   |2017-11-29 |CRAN (R 3.5.0)                      |
+|wilson          |   |2.0.0   |2018-06-27 |local (HendrikSchultheis/wilson@NA) |
+
+# Check results
+
+0 packages with problems
+
+
+
+
diff --git a/revdep/timing.md b/revdep/timing.md
new file mode 100644
index 0000000..59483ca
--- /dev/null
+++ b/revdep/timing.md
@@ -0,0 +1,5 @@
+# Check times
+
+
+
+

From 53ab467adc94661a7d9436fd373dd84a0dc64ba4 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 08:21:31 +0200
Subject: [PATCH 44/75] lint and

---
 R/and.R | 130 ++++++++++++++++++++++++++++----------------------------
 1 file changed, 65 insertions(+), 65 deletions(-)

diff --git a/R/and.R b/R/and.R
index f37bcf2..13e8e98 100644
--- a/R/and.R
+++ b/R/and.R
@@ -38,8 +38,8 @@ andUI <- function(id) {
 #' @export
 and <- function(input, output, session, data, show.elements = NULL, element.grouping = NULL, column.labels = NULL, delimiter = NULL, multiple = TRUE, contains = FALSE, ranged = FALSE, step = 100, reset = NULL) {
   # handle reactive data
-  data.r <- shiny::reactive({
-    if(shiny::is.reactive(data)){
+  data_r <- shiny::reactive({
+    if (shiny::is.reactive(data)) {
       data()
     }else{
       data
@@ -47,69 +47,69 @@ and <- function(input, output, session, data, show.elements = NULL, element.grou
   })
 
   # handle reactive show.elements
-  show.elements.r <- shiny::reactive({
-    if(shiny::is.reactive(show.elements)) {
+  show_elements_r <- shiny::reactive({
+    if (shiny::is.reactive(show.elements)) {
       show.elements <- show.elements()
     } else {
       show.elements <- show.elements
     }
-    if(is.null(show.elements)) {
-      show.elements <- names(data.r())
+    if (is.null(show.elements)) {
+      show.elements <- names(data_r())
     }
 
     return(show.elements)
   })
 
   # handle reactive grouping
-  element.grouping.r <- shiny::reactive({
-    if(shiny::is.reactive(element.grouping)){
+  element_grouping_r <- shiny::reactive({
+    if (shiny::is.reactive(element.grouping)) {
       element.grouping()
-    }else{
+    } else {
       element.grouping
     }
   })
 
   parameter <- shiny::reactive({
     # get column labels
-    if(is.null(column.labels)){
-      column.labels <- names(data.r())
-    }else{
+    if (is.null(column.labels)) {
+      column.labels <- names(data_r())
+    } else {
       column.labels <- column.labels
     }
     # fill multiple if vector is too small
-    if(shiny::is.reactive(multiple)) {
+    if (shiny::is.reactive(multiple)) {
       multiple <- multiple()
     }
-    if (length(multiple) < ncol(data.r())) {
-      multiple <- rep(multiple, length.out = ncol(data.r()))
+    if (length(multiple) < ncol(data_r())) {
+      multiple <- rep(multiple, length.out = ncol(data_r()))
     }
     # fill contains if vector is too small
-    if(shiny::is.reactive(contains)) {
+    if (shiny::is.reactive(contains)) {
       contains <- contains()
     }
-    if (length(contains) < ncol(data.r())) {
-      contains <- rep(contains, length.out = ncol(data.r()))
+    if (length(contains) < ncol(data_r())) {
+      contains <- rep(contains, length.out = ncol(data_r()))
     }
     # fill ranged if vector is too small
-    if(shiny::is.reactive(ranged)) {
+    if (shiny::is.reactive(ranged)) {
       ranged <- ranged()
     }
-    if (length(ranged) < ncol(data.r())) {
-      ranged <- rep(ranged, length.out = ncol(data.r()))
+    if (length(ranged) < ncol(data_r())) {
+      ranged <- rep(ranged, length.out = ncol(data_r()))
     }
     # fill delimiter if vector is too small
-    if(shiny::is.reactive(delimiter)) {
+    if (shiny::is.reactive(delimiter)) {
       delimiter <- delimiter()
     }
-    if (length(delimiter) < ncol(data.r()) & !is.null(delimiter)) {
-      delimiter <- rep(delimiter, length.out = ncol(data.r()))
+    if (length(delimiter) < ncol(data_r()) & !is.null(delimiter)) {
+      delimiter <- rep(delimiter, length.out = ncol(data_r()))
     }
     # fill step if vector is too small
-    if(shiny::is.reactive(step)) {
+    if (shiny::is.reactive(step)) {
       step <- step()
     }
-    if (length(step) < ncol(data.r()) & !is.null(step)) {
-      step <- rep(step, length.out = ncol(data.r()))
+    if (length(step) < ncol(data_r()) & !is.null(step)) {
+      step <- rep(step, length.out = ncol(data_r()))
     }
 
     return(list(column.labels = column.labels, multiple = multiple, contains = contains, ranged = ranged, delimiter = delimiter, step = step))
@@ -122,15 +122,15 @@ and <- function(input, output, session, data, show.elements = NULL, element.grou
     progress$set(0, message = "Render orModules:")
 
     # select data based on show.elements
-    data <- data.r()[, show.elements.r(), with = FALSE]
+    data <- data_r()[, show_elements_r(), with = FALSE]
 
     step <- ncol(data)
 
-    if(!is.null(element.grouping.r())){
+    if (!is.null(element_grouping_r())) {
       # only group shown data
-      element.grouping <- element.grouping.r()[element.grouping.r()[[1]] %in% show.elements.r()]
+      element.grouping <- element_grouping_r()[element_grouping_r()[[1]] %in% show_elements_r()]
 
-      grouping <- tapply(element.grouping[[1]], element.grouping[[2]], function(x){x})
+      grouping <- tapply(element.grouping[[1]], element.grouping[[2]], function(x) {x})
       # keep grouping order
       grouping <- grouping[unique(element.grouping[[2]])]
 
@@ -138,19 +138,19 @@ and <- function(input, output, session, data, show.elements = NULL, element.grou
         group <- lapply(unlist(grouping[i]), function(x){
           progress$inc(step, detail = x)
 
-          if(is.numeric(data[[x]])){
+          if (is.numeric(data[[x]])) {
             ui <- orNumericUI(id = session$ns(openssl::sha1(x)))
-          }else{
+          } else {
             ui <- orTextualUI(id = session$ns(openssl::sha1(x)))
           }
 
-          if(length(ui) < 4){ # orTextual
+          if (length(ui) < 4) { # orTextual
             shiny::tagList(shiny::fluidRow(
               shiny::column(width = 4, ui[1]),
               shiny::column(width = 3, ui[2]),
               shiny::column(width = 1, offset = 4, ui[3])
             ))
-          }else{ # orNumeric
+          } else { # orNumeric
             shiny::tagList(shiny::fluidRow(
               shiny::column(width = 4, ui[1]),
               shiny::column(width = 1, ui[2]),
@@ -163,23 +163,23 @@ and <- function(input, output, session, data, show.elements = NULL, element.grou
 
         shiny::tagList(shinydashboard::box(width = 12, collapsible = TRUE, collapsed = TRUE, title = names(grouping[i]), shiny::tagList(group)))
       })
-    }else{
+    } else {
       return <- lapply(1:ncol(data), function(x) {
         progress$inc(step, detail = names(data)[x])
         if (is.numeric(data[[x]])) {
           ui <- orNumericUI(id = session$ns(openssl::sha1(names(data)[x])))
 
-        } else{
+        } else {
           ui <- orTextualUI(id = session$ns(openssl::sha1(names(data)[x])))
         }
 
-        if(length(ui) < 4){ # orTextual
+        if (length(ui) < 4) { # orTextual
           shiny::tagList(shiny::fluidRow(
             shiny::column(width = 4, ui[1]),
             shiny::column(width = 3, ui[2]),
             shiny::column(width = 1, offset = 4, ui[3])
           ))
-        }else{ # orNumeric
+        } else { # orNumeric
           shiny::tagList(shiny::fluidRow(
             shiny::column(width = 4, ui[1]),
             shiny::column(width = 1, ui[2]),
@@ -203,41 +203,41 @@ and <- function(input, output, session, data, show.elements = NULL, element.grou
     progress <- shiny::Progress$new()
     on.exit(progress$close())
     progress$set(0, message = "Filtering Module:")
-    step <- ncol(data.r())
+    step <- ncol(data_r())
 
-    lapply(1:ncol(data.r()), function(x) {
-      progress$inc(step, detail = names(data.r())[x])
-      if (is.numeric(data.r()[[x]])) {
+    lapply(1:ncol(data_r()), function(x) {
+      progress$inc(step, detail = names(data_r())[x])
+      if (is.numeric(data_r()[[x]])) {
         if (parameter()$ranged[x]) {
           shiny::callModule(
             module = orNumeric,
-            id = openssl::sha1(names(data.r())[x]),
-            choices = data.r()[[x]],
-            value = c(floor(min(data.r()[[x]], na.rm = TRUE)), ceiling(max(data.r()[[x]], na.rm = TRUE))),
+            id = openssl::sha1(names(data_r())[x]),
+            choices = data_r()[[x]],
+            value = c(floor(min(data_r()[[x]], na.rm = TRUE)), ceiling(max(data_r()[[x]], na.rm = TRUE))),
             label = parameter()$column.labels[x],
             step = parameter()$step[x],
-            min. = floor(min(data.r()[[x]], na.rm = TRUE)),
-            max. = ceiling(max(data.r()[[x]], na.rm = TRUE)),
+            min. = floor(min(data_r()[[x]], na.rm = TRUE)),
+            max. = ceiling(max(data_r()[[x]], na.rm = TRUE)),
             reset = reset
           )
         } else{
           shiny::callModule(
             module = orNumeric,
-            id = openssl::sha1(names(data.r())[x]),
-            choices = data.r()[[x]],
-            value = mean(data.r()[[x]], na.rm = TRUE),
+            id = openssl::sha1(names(data_r())[x]),
+            choices = data_r()[[x]],
+            value = mean(data_r()[[x]], na.rm = TRUE),
             label = parameter()$column.labels[x],
             step = parameter()$step[x],
-            min. = floor(min(data.r()[[x]], na.rm = TRUE)),
-            max. = ceiling(max(data.r()[[x]], na.rm = TRUE)),
+            min. = floor(min(data_r()[[x]], na.rm = TRUE)),
+            max. = ceiling(max(data_r()[[x]], na.rm = TRUE)),
             reset = reset
           )
         }
       } else{
         shiny::callModule(
           module = orTextual,
-          id = openssl::sha1(names(data.r())[x]),
-          choices = as.character(data.r()[[x]]),
+          id = openssl::sha1(names(data_r())[x]),
+          choices = as.character(data_r()[[x]]),
           label = parameter()$column.labels[x],
           delimiter = parameter()$delimiter[x],
           multiple = parameter()$multiple[x],
@@ -256,35 +256,35 @@ and <- function(input, output, session, data, show.elements = NULL, element.grou
 
     log_message(message = "Applying filter...", level = "INFO", token = session$token)
 
-    or.modules <- modules()
+    or_modules <- modules()
 
-    step <- 0.9 / length(or.modules)
+    step <- 0.9 / length(or_modules)
     # OR modules selection
-    or.selection.bool <- sapply(or.modules, function(x) {
+    or_selection_bool <- sapply(or_modules, function(x) {
       progress$inc(step, detail = x()$label)
       x()$bool
     })
-    or.selection.text <- sapply(or.modules, function(x) {
-      if(shiny::isTruthy(x()$text)){
+    or_selection_text <- sapply(or_modules, function(x) {
+      if (shiny::isTruthy(x()$text)) {
         return(paste0(x()$label, ": ", paste(x()$text, collapse = ","), collapse = ""))
       }
     })
 
     # cast to matrix if sapply returns vector
-    if(is.vector(or.selection.bool)){
-      or.selection.bool <- t(as.matrix(or.selection.bool))
+    if (is.vector(or_selection_bool)) {
+      or_selection_bool <- t(as.matrix(or_selection_bool))
     }
 
     # selected rows (and selection)
-    and.selection.bool <- apply(or.selection.bool, 1, all)
+    and_selection_bool <- apply(or_selection_bool, 1, all)
 
-    or.selection.text <- unlist(or.selection.text)
+    or_selection_text <- unlist(or_selection_text)
 
     progress$set(1)
 
     log_message(message = "Done.", level = "INFO", token = session$token)
 
-    return(list(bool = and.selection.bool, text = unlist(or.selection.text)))
+    return(list(bool = and_selection_bool, text = unlist(or_selection_text)))
   })
 
   return(selection)

From 2524e04f9bde32b6064ba4a2f4d94ee2976a0925 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 08:30:19 +0200
Subject: [PATCH 45/75] lint clarion

---
 R/clarion.R    | 30 +++++++++++++++---------------
 man/Clarion.Rd |  4 ++--
 2 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/R/clarion.R b/R/clarion.R
index ada66a0..f9ebe6c 100644
--- a/R/clarion.R
+++ b/R/clarion.R
@@ -5,8 +5,8 @@
 #'
 #' @section Methods:
 #' \describe{
-#'     \item{\code{get_uniqueID()}}{
-#'       Returns name of unique column. Assumes first feature to be unique if not specified.
+#'     \item{\code{get_id()}}{
+#'       Returns name of unique identifier column. Assumes first feature to be unique if not specified.
 #'     }
 #'     \item{\code{get_name()}}{
 #'       Returns name of name column. If not specified return unique Id.
@@ -51,7 +51,7 @@ Clarion <- R6::R6Class("Clarion",
                          header = NULL,
                          metadata = NULL,
                          data = NULL,
-                         get_uniqueID = function() {
+                         get_id = function() {
                            # return unique_id
                            # if no type return first feature
                            if (is.element("type", names(self$metadata))) {
@@ -66,7 +66,7 @@ Clarion <- R6::R6Class("Clarion",
                            if (is.element("type", names(self$metadata)) && is.element("name", self$metadata[["type"]])) {
                              return(self$metadata[type == "name"][["key"]])
                            }
-                           return(self$get_uniqueID())
+                           return(self$get_uniqueid())
                          },
                          get_delimiter = function() {
                            self$header$delimiter
@@ -101,15 +101,15 @@ Clarion <- R6::R6Class("Clarion",
                            # validate header
                            private$check_delimiter()
                            # validate metadata
-                           private$check_metadataHeader()
+                           private$check_metadata_header()
                            private$check_key()
                            private$check_level()
                            private$check_type()
                            private$check_label()
                            # validate data
-                           private$check_dataHeader(solve)
-                           private$check_dataMin()
-                           private$check_dataColumnTypes()
+                           private$check_data_header(solve)
+                           private$check_data_min()
+                           private$check_data_column_types()
                          },
                          initialize = function(header = NULL, metadata, data, validate = TRUE) {
                            self$header <- header
@@ -117,10 +117,10 @@ Clarion <- R6::R6Class("Clarion",
                            self$data <- data
 
                            # coerce unique_id and name to character
-                           if (self$get_uniqueID() == self$get_name()) {
-                             cols <- self$get_uniqueID()
+                           if (self$get_id() == self$get_name()) {
+                             cols <- self$get_id()
                            } else {
-                             cols <- c(self$get_uniqueID(), self$get_name())
+                             cols <- c(self$get_id(), self$get_name())
                            }
                            self$data[, (cols) := lapply(.SD, as.character), .SDcols = cols]
 
@@ -147,7 +147,7 @@ Clarion <- R6::R6Class("Clarion",
                            }
                          },
                          ## metadata checks
-                         check_metadataHeader = function() {
+                         check_metadata_header = function() {
                            # case: invalid column names
                            valid_names <- c("key", "factor\\d+(=\".*\")?", "level", "type", "label", "sub_label")
                            regex <- paste0("^", valid_names, "$", collapse = "|")
@@ -216,7 +216,7 @@ Clarion <- R6::R6Class("Clarion",
                            }
                          },
                          ## data checks
-                         check_dataHeader = function(solve = TRUE) {
+                         check_data_header = function(solve = TRUE) {
                            # case: column not defined in metadata
                            missing <- setdiff(names(self$data), self$metadata[["key"]])
                            if (length(missing) > 0) {
@@ -231,13 +231,13 @@ Clarion <- R6::R6Class("Clarion",
                              stop("Data: Column names not unique! Following names occur more than once: ", paste0(unique(names(self$data)[duplicated(names(self$data))]), collapse = ", "))
                            }
                          },
-                         check_dataMin = function() {
+                         check_data_min = function() {
                            # case: minimum requirements not met (two columns: feature(unique_id) + sample|condition|contrast)
                            if (ncol(self$data) < 2) {
                              stop("Data: Minimum requirements not met! At least two columns needed, one with unique identifier and one with numeric values.")
                            }
                          },
-                         check_dataColumnTypes = function() {
+                         check_data_column_types = function() {
                            # case: level = sample, condition, contrast not numeric
                            # except type=array because of delimiter
                            if (is.element("type", names(self$metadata))) {
diff --git a/man/Clarion.Rd b/man/Clarion.Rd
index 8c0f4aa..43df4ff 100644
--- a/man/Clarion.Rd
+++ b/man/Clarion.Rd
@@ -30,8 +30,8 @@ This object is used by all top-level wilson modules.
 \section{Methods}{
 
 \describe{
-    \item{\code{get_uniqueID()}}{
-      Returns name of unique column. Assumes first feature to be unique if not specified.
+    \item{\code{get_id()}}{
+      Returns name of unique identifier column. Assumes first feature to be unique if not specified.
     }
     \item{\code{get_name()}}{
       Returns name of name column. If not specified return unique Id.

From 1c3ca984abb4a7070a4c4532514dcd0cf550b0ae Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 08:48:49 +0200
Subject: [PATCH 46/75] lint colorPicker

---
 R/colorPicker.R | 121 ++++++++++++++++++++++++------------------------
 1 file changed, 60 insertions(+), 61 deletions(-)

diff --git a/R/colorPicker.R b/R/colorPicker.R
index 6297397..5825e12 100644
--- a/R/colorPicker.R
+++ b/R/colorPicker.R
@@ -17,10 +17,10 @@
 colorPickerUI <- function(id, label = "Color scheme", custom = FALSE, multiple = FALSE, show.reverse = TRUE, show.scaleoptions = TRUE, show.transparency = TRUE) {
   ns <- shiny::NS(id)
 
-  if(custom){
+  if (custom) {
     ret <- list(colourpicker::colourInput(ns("picker"), label = NULL, value = "red"))
 
-    if(multiple){
+    if (multiple) {
       ret <- list(
         shinyjs::useShinyjs(),
         shiny::textInput(ns("palette"), label = NULL, value = "red,blue", placeholder = "e.g. black,#3c8dbc"),
@@ -31,18 +31,18 @@ colorPickerUI <- function(id, label = "Color scheme", custom = FALSE, multiple =
     }
 
     ret <- list(shiny::tags$b(label), ret)
-  }else{
+  } else {
     ret <- list(shiny::tags$b(label), shiny::uiOutput(ns("palette")))
   }
 
-  if(!custom | custom & multiple){
-    if(show.reverse) {
+  if (!custom | custom & multiple) {
+    if (show.reverse) {
       ret <- c(ret, list(shiny::checkboxInput(ns("reverse"), label = "Reverse scheme")))
     }
-    if(show.scaleoptions) {
+    if (show.scaleoptions) {
       ret <- c(ret, limitUI(ns("winsorize"), label = "Winsorize to upper/lower"))
     }
-    if(show.transparency) {
+    if (show.transparency) {
       ret <- c(ret, list(shiny::sliderInput(ns("transparency"), label = "Transparency", min = 0, max = 1, value = 1)))
     }
   }
@@ -76,34 +76,34 @@ colorPicker <- function(input, output, session, num.colors = 256, distribution =
   shinyjs::reset("reverse")
   shinyjs::reset("transparency")
 
-  #handle reactive distribution
-  distribution.r <- shiny::reactive({
-    if(shiny::is.reactive(distribution)){
+  # handle reactive distribution
+  distribution_r <- shiny::reactive({
+    if (shiny::is.reactive(distribution)) {
       distribution()
-    }else{
+    } else {
       distribution
     }
   })
 
-  if(!is.null(winsorize)) {
+  if (!is.null(winsorize)) {
     # handle reactive winsorize
-    winsorize.r <- shiny::reactive({
-      if(shiny::is.reactive(winsorize)) {
+    winsorize_r <- shiny::reactive({
+      if (shiny::is.reactive(winsorize)) {
         winsorize()
       } else {
         winsorize
       }
     })
   }
-  limits <- shiny::callModule(limit, "winsorize", lower = if(!is.null(winsorize)){shiny::reactive(winsorize.r()[1])}, upper = if(!is.null(winsorize)){shiny::reactive(winsorize.r()[2])})
+  limits <- shiny::callModule(limit, "winsorize", lower = if (!is.null(winsorize)) {shiny::reactive(winsorize_r()[1])}, upper = if (!is.null(winsorize)) {shiny::reactive(winsorize_r()[2])})
 
   output$palette <- shiny::renderUI({
     choices <- list()
 
-    if("sequential" %in% distribution.r()) choices <- append(choices, list(Sequential = names(Sequential)))
-    if("diverging" %in% distribution.r()) choices <- append(choices, list(Diverging = names(Diverging)))
-    if("categorical" %in% distribution.r()) choices <- append(choices, list(Categorical = names(Categorical)))
-    if(length(distribution.r()) == 1 && distribution.r() == "all") {
+    if ("sequential" %in% distribution_r()) choices <- append(choices, list(Sequential = names(Sequential)))
+    if ("diverging" %in% distribution_r()) choices <- append(choices, list(Diverging = names(Diverging)))
+    if ("categorical" %in% distribution_r()) choices <- append(choices, list(Categorical = names(Categorical)))
+    if (length(distribution_r()) == 1 && distribution_r() == "all") {
       choices <- list(Sequential = names(Sequential), Diverging = names(Diverging), Categorical = names(Categorical))
     }
 
@@ -120,26 +120,26 @@ colorPicker <- function(input, output, session, num.colors = 256, distribution =
     shiny::updateTextInput(session, "palette", value = "")
   })
 
-  #create custom colorpalette
+  # create custom colorpalette
   custom <- shiny::reactive({
-    #returns TRUE if String is a valid color
-    isColor <- function(x){
-      res <- try(grDevices::col2rgb(x),silent=TRUE)
-      return(!"try-error"%in%class(res))
+    # returns TRUE if String is a valid color
+    is_color <- function(x){
+      res <- try(grDevices::col2rgb(x), silent = TRUE)
+      return(!"try-error" %in% class(res))
     }
 
     pal <- unlist(strsplit(input$palette, split = ",", fixed = TRUE))
 
-    if(length(pal) != 0){
-      valid <- unlist(lapply(pal, isColor))
-      if(!all(valid)){
+    if (length(pal) != 0) {
+      valid <- unlist(lapply(pal, is_color))
+      if (!all(valid)) {
         shiny::showNotification(id = session$ns("notification"), shiny::HTML(paste("<b>ColorPicker</b><br/> Found invalid colors: ", paste(pal[!valid], collapse = ", "))), duration = NULL, type = "warning")
         pal <- NULL
-      }else{
+      } else {
         shiny::removeNotification(id = session$ns("notification"))
         pal <- grDevices::colorRampPalette(pal)(num.colors)
       }
-    }else{
+    } else {
       shiny::showNotification(id = session$ns("notification"), shiny::HTML("<b>ColorPicker</b><br/> Warning no colors selected!"), duration = NULL, type = "warning")
       pal <- NULL
     }
@@ -148,34 +148,34 @@ colorPicker <- function(input, output, session, num.colors = 256, distribution =
   })
 
   output <- shiny::reactive({
-    if(is.null(input$palette)){
-      #custom single color
+    if (is.null(input$palette)) {
+      # custom single color
       pal <- input$picker
     }else{
-      #predefined palettes
-      if(is.null(shiny::isolate(input$picker))){
-        #get palette
-        if(input$palette %in% names(Sequential)){
+      # predefined palettes
+      if (is.null(shiny::isolate(input$picker))) {
+        # get palette
+        if (input$palette %in% names(Sequential)) {
           pal <- Sequential[[input$palette]]
-        }else if(input$palette %in% names(Diverging)){
+        } else if (input$palette %in% names(Diverging)) {
           pal <- Diverging[[input$palette]]
-        }else {
+        } else {
           pal <- Categorical[[input$palette]]
         }
-      }else{
-        #custom palettes (multiple colors)
+      } else {
+        # custom palettes (multiple colors)
         pal <- custom()
       }
-      #reverse palette
-      if(!is.null(input$reverse)){
-        if(input$reverse){
+      # reverse palette
+      if (!is.null(input$reverse)) {
+        if (input$reverse) {
           pal <- rev(pal)
         }
       }
     }
 
     winsorize <- NULL
-    if(!is.null(limits())) {
+    if (!is.null(limits())) {
       winsorize <- c(limits()$lower, limits()$upper)
     }
 
@@ -199,19 +199,19 @@ colorPicker <- function(input, output, session, num.colors = 256, distribution =
 #'
 sequentialPalettes <- function(n) {
   Heat <- grDevices::colorRampPalette(rev(RColorBrewer::brewer.pal(9, "YlOrRd")))(n)
-  Viridis	<- viridis::viridis(n)
+  Viridis <- viridis::viridis(n)
   Magma <- viridis::magma(n)
-  Inferno	<- viridis::inferno(n)
+  Inferno <- viridis::inferno(n)
   Plasma <- viridis::plasma(n)
   YlGnBu <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "YlGnBu"))(n)
   Blues <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "Blues"))(n)
   Reds <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "Reds"))(n)
-  Cubehelix	<- rje::cubeHelix(n)
+  Cubehelix <- rje::cubeHelix(n)
 
-  BkOrYl <- grDevices::colorRampPalette(c("black", "orange", "yellow"))(n)						#one-sided (0 .. x): go enrichment
-  GnBu <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "GnBu"))(n)							#one-sided (0 .. x): expression
-  PuBuGn <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "PuBuGn"))(n)							#one-sided (0 .. x): expression
-  BuGnYlRd <- grDevices::colorRampPalette(c("#000041", "#0000CB", "#0081FF", "#02DA81", "#80FE1A", "#FDEE02", "#FFAB00", "#FF3300"))(n)	#one-sided (0 .. x): expression, ~=spectral
+  BkOrYl <- grDevices::colorRampPalette(c("black", "orange", "yellow"))(n)						# one-sided (0 .. x): go enrichment
+  # GnBu <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "GnBu"))(n)							# one-sided (0 .. x): expression
+  PuBuGn <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "PuBuGn"))(n)							# one-sided (0 .. x): expression
+  # BuGnYlRd <- grDevices::colorRampPalette(c("#000041", "#0000CB", "#0081FF", "#02DA81", "#80FE1A", "#FDEE02", "#FFAB00", "#FF3300"))(n)	# one-sided (0 .. x): expression, ~=spectral
 
   data.table::data.table(Heat, Viridis, Magma, Inferno, Plasma, YlGnBu, Blues, Reds, Cubehelix, BkOrYl, PuBuGn)
 }
@@ -225,18 +225,18 @@ sequentialPalettes <- function(n) {
 divergingPalettes <- function(n) {
   BuWtRd <- grDevices::colorRampPalette(c("royalblue4", "steelblue4", "white", "indianred", "firebrick4"))(n)
   RdBkGr <- gplots::redgreen(n)
-  RdYlGr <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "RdYlGn"))(n)
-  YlWtPu <- grDevices::colorRampPalette(c("gold", "white", "white", "mediumpurple4"))(n)					#two-sided (-1 .. +1): correlation
+  # RdYlGr <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "RdYlGn"))(n)
+  YlWtPu <- grDevices::colorRampPalette(c("gold", "white", "white", "mediumpurple4"))(n)					# two-sided (-1 .. +1): correlation
   Spectral <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "Spectral"))(n)
 
-  BuYlGn <- grDevices::colorRampPalette(c("dodgerblue4", "cadetblue1", "yellow", "darkolivegreen1", "darkgreen"))(n)	#two-sided (-x .. +x): fold-change
-  TqWtRd <- grDevices::colorRampPalette(c("darkslategray", "darkturquoise", "cornsilk", "indianred3", "red3"))(n)		#two-sided (-x .. +x): fold-change
-  YlGyRd <- grDevices::colorRampPalette(c("yellow", "grey25", "red"))(n)							#two-sided (-x .. +x): fold-change
-  RdBu <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "RdBu"))(n)							#two-sided (-x .. +x): fold-change
-  GnWtRd <- grDevices::colorRampPalette(c("chartreuse3", "white", "firebrick1"))(n)					#two-sided (-x .. +x): fold-change
-  RdYlBu <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "RdYlBu"))(n)							#two-sided (-x .. +x): fold-change
-  RdGy <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "RdGy"))(n)							#two-sided (-x .. +x): fold-change
-  PuOr <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "PuOr"))(n)							#two-sided (-x .. +x): fold-change
+  BuYlGn <- grDevices::colorRampPalette(c("dodgerblue4", "cadetblue1", "yellow", "darkolivegreen1", "darkgreen"))(n)	# two-sided (-x .. +x): fold-change
+  # TqWtRd <- grDevices::colorRampPalette(c("darkslategray", "darkturquoise", "cornsilk", "indianred3", "red3"))(n)		# two-sided (-x .. +x): fold-change
+  # YlGyRd <- grDevices::colorRampPalette(c("yellow", "grey25", "red"))(n)							# two-sided (-x .. +x): fold-change
+  # RdBu <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "RdBu"))(n)							# two-sided (-x .. +x): fold-change
+  GnWtRd <- grDevices::colorRampPalette(c("chartreuse3", "white", "firebrick1"))(n)					# two-sided (-x .. +x): fold-change
+  # RdYlBu <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "RdYlBu"))(n)							# two-sided (-x .. +x): fold-change
+  RdGy <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "RdGy"))(n)							# two-sided (-x .. +x): fold-change
+  PuOr <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(11, "PuOr"))(n)							# two-sided (-x .. +x): fold-change
 
   data.table::data.table(BuWtRd, Spectral, RdBkGr, YlWtPu, BuYlGn, GnWtRd, RdGy, PuOr)
 }
@@ -259,4 +259,3 @@ categoricalPalettes <- function(n) {
 
   data.table::data.table(Accent, Dark2, Paired, Pastel1, Pastel2, Set1, Set2, Set3)
 }
-

From 9656bbd1da47e85e87f4addca9252c2f3c2b2e8a Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 09:16:03 +0200
Subject: [PATCH 47/75] lint columnSelector + example

---
 R/columnSelector.R            | 82 +++++++++++++++++------------------
 exec/columnSelector_example.R | 11 +++--
 man/columnSelector.Rd         | 10 ++---
 3 files changed, 51 insertions(+), 52 deletions(-)

diff --git a/R/columnSelector.R b/R/columnSelector.R
index 0c5c299..0130eff 100644
--- a/R/columnSelector.R
+++ b/R/columnSelector.R
@@ -8,7 +8,7 @@
 #'
 #' @export
 columnSelectorUI <- function(id, label = F, title = NULL) {
-  #create namespace
+  # create namespace
   ns <- shiny::NS(id)
 
   shiny::tagList(
@@ -16,7 +16,7 @@ columnSelectorUI <- function(id, label = F, title = NULL) {
     shinyjs::useShinyjs(),
     shiny::singleton(shiny::tags$head(shiny::tags$link(rel = "stylesheet", type = "text/css", href = "wilson_www/styles.css"))),
     shiny::uiOutput(ns("out")),
-    {if(label) shiny::uiOutput(ns("showLabel"))}
+    if (label) shiny::uiOutput(ns("show_label"))
   )
 }
 
@@ -31,26 +31,26 @@ columnSelectorUI <- function(id, label = F, title = NULL) {
 #'                                label = optional, used instead of id
 #'                                sub_label = optional, added to id/ label
 #' @param type The type (contrast/group/sample of the type dropdown menu, selected in step 1 (upper dropdown). Defaults to unique(type.columns[,2]) (Supports reactive)
-#' @param columnTypeLabel Changes the label of the first UI element
-#' @param labelLabel Change label above label text input.
+#' @param column.type.tabel Changes the label of the first UI element
+#' @param label.label Change label above label text input.
 #' @param multiple Boolean value whether multiple values can be selected in second selector. (Default = TRUE)
 #' @param none If TRUE adds "None to secondSelector and select is. (Default = FALSE)
 #' @param sep Used to separate labels on multi value selection.
 #' @param suffix Added to label only on multiple = FALSE (supports reactive). Also uses sep as separator.
 #'
-#' @return Returns the input. As named list: names("type", "selectedColumns", "label")
+#' @return Returns the input. As named list: names("type", "selected_columns", "label")
 #'
 #' @export
-columnSelector <- function(input, output, session, type.columns, type = NULL, columnTypeLabel = "Type of Column", labelLabel = "Label", multiple = TRUE, none = FALSE, sep = ", ", suffix = NULL) {
+columnSelector <- function(input, output, session, type.columns, type = NULL, column.type.label = "Type of Column", label.label = "Label", multiple = TRUE, none = FALSE, sep = ", ", suffix = NULL) {
   # handle reactive input
-  type.columns.r <- shiny::reactive({
+  type_columns_r <- shiny::reactive({
     if (shiny::is.reactive(type.columns)) {
       type.columns()
     } else {
       type.columns
     }
   })
-  type.r <- shiny::reactive({
+  type_r <- shiny::reactive({
     if (!is.null(type)) {
       if (shiny::is.reactive(type)) {
         type()
@@ -58,10 +58,10 @@ columnSelector <- function(input, output, session, type.columns, type = NULL, co
         type
       }
     } else {
-      unique(type.columns.r()[[2]])
+      unique(type_columns_r()[[2]])
     }
   })
-  suffix.r <- shiny::reactive({
+  suffix_r <- shiny::reactive({
     if (shiny::is.reactive(suffix)) {
       suffix()
     } else {
@@ -71,46 +71,46 @@ columnSelector <- function(input, output, session, type.columns, type = NULL, co
 
   output$out <- shiny::renderUI({
     if (none) {
-      choices <- c("None", type.columns.r()[type.columns.r()[["level"]] %in% type.r()[1]][["key"]])
+      choices <- c("None", type_columns_r()[type_columns_r()[["level"]] %in% type_r()[1]][["key"]])
     }else{
-      choices <- type.columns.r()[type.columns.r()[["level"]] %in% type.r()[1]][["key"]]
+      choices <- type_columns_r()[type_columns_r()[["level"]] %in% type_r()[1]][["key"]]
     }
-    columnSelectLabel = "Select individual column"
+    column_select_label <- "Select individual column"
     if (multiple) {
-      columnSelectLabel = paste0(columnSelectLabel, "(s)")
+      column_select_label <- paste0(column_select_label, "(s)")
     }
 
     shiny::tagList(
-      shiny::selectInput(session$ns("select.type"), label = columnTypeLabel, choices = type.r(), selected = type.r()[1], multiple = FALSE),
-      shiny::div(shiny::selectizeInput(session$ns("select.column"), label = columnSelectLabel, choices = choices, multiple = multiple), class = "empty") # colored background if empty
+      shiny::selectInput(session$ns("select_type"), label = column.type.label, choices = type_r(), selected = type_r()[1], multiple = FALSE),
+      shiny::div(shiny::selectizeInput(session$ns("select_column"), label = column_select_label, choices = choices, multiple = multiple), class = "empty") # colored background if empty
     )
   })
 
   # show label textInput
-  output$showLabel <- shiny::renderUI({
-    shiny::textInput(session$ns("select.label"), label = labelLabel)
+  output$show_label <- shiny::renderUI({
+    shiny::textInput(session$ns("select_label"), label = label.label)
   })
 
   # make label
   create_label <- shiny::reactive({
-    shiny::req(input$select.type)
+    shiny::req(input$select_type)
     # empty label on 'None'
-    if (none && input$select.column == "None") return("")
+    if (none && input$select_column == "None") return("")
 
-    if (is.element("label", names(type.columns.r()))) {
-      label_id <- input$select.column
-      label_label <- type.columns.r()[type.columns.r()[["key"]] %in% input$select.column][["label"]]
+    if (is.element("label", names(type_columns_r()))) {
+      label_id <- input$select_column
+      label_label <- type_columns_r()[type_columns_r()[["key"]] %in% input$select_column][["label"]]
 
       # replace id with label
       label <- ifelse(label_label == "", label_id, label_label)
 
     } else {
-      label <- input$select.column
+      label <- input$select_column
     }
 
     # add sub_label
-    if (is.element("sub_label", names(type.columns.r()))) {
-      label <- paste(label, type.columns.r()[type.columns.r()[["key"]] %in% input$select.column][["sub_label"]])
+    if (is.element("sub_label", names(type_columns_r()))) {
+      label <- paste(label, type_columns_r()[type_columns_r()[["key"]] %in% input$select_column][["sub_label"]])
     }
 
     label <- paste(label, collapse = sep)
@@ -120,17 +120,17 @@ columnSelector <- function(input, output, session, type.columns, type = NULL, co
 
   # update label
   shiny::observe({
-    input$select.column
-    suffix.r()
+    input$select_column
+    suffix_r()
 
     shiny::isolate({
-      if (!is.null(input$select.label)) {
-        if (!multiple && !is.null(suffix.r())) {
-          value <- paste(create_label(), suffix.r(), sep = sep)
+      if (!is.null(input$select_label)) {
+        if (!multiple && !is.null(suffix_r())) {
+          value <- paste(create_label(), suffix_r(), sep = sep)
         } else {
           value <- create_label()
         }
-        shiny::updateTextInput(session = session, inputId = "select.label", value = value)
+        shiny::updateTextInput(session = session, inputId = "select_label", value = value)
       }
     })
   })
@@ -138,21 +138,21 @@ columnSelector <- function(input, output, session, type.columns, type = NULL, co
   # show columns based on selected type
   shiny::observe({
     if (none) {
-      columns <- c("None", type.columns.r()[type.columns.r()[["level"]] %in% input$select.type][["key"]])
+      columns <- c("None", type_columns_r()[type_columns_r()[["level"]] %in% input$select_type][["key"]])
     } else {
-      columns <- type.columns.r()[type.columns.r()[["level"]] %in% input$select.type][["key"]]
+      columns <- type_columns_r()[type_columns_r()[["level"]] %in% input$select_type][["key"]]
     }
 
-    shiny::updateSelectizeInput(session = session, inputId = "select.column", choices = columns)
+    shiny::updateSelectizeInput(session = session, inputId = "select_column", choices = columns)
   })
 
-  out.type <- shiny::reactive(input$select.type)
-  out.selectedColumns <- shiny::reactive(if (shiny::isTruthy(input$select.column) && input$select.column != "None") input$select.column else "")
-  out.label <- shiny::reactive({
-    if (is.null(input$select.label)) {
+  out_type <- shiny::reactive(input$select_type)
+  out_selected_columns <- shiny::reactive(if (shiny::isTruthy(input$select_column) && input$select_column != "None") input$select_column else "")
+  out_label <- shiny::reactive({
+    if (is.null(input$select_label)) {
       label <- create_label()
     } else {
-      label <- input$select.label
+      label <- input$select_label
     }
 
     if (multiple) {
@@ -162,5 +162,5 @@ columnSelector <- function(input, output, session, type.columns, type = NULL, co
     return(label)
   })
 
-  return(list(type = out.type, selectedColumns = out.selectedColumns, label = out.label))
+  return(list(type = out_type, selected_columns = out_selected_columns, label = out_label))
 }
diff --git a/exec/columnSelector_example.R b/exec/columnSelector_example.R
index 6609afc..3641471 100644
--- a/exec/columnSelector_example.R
+++ b/exec/columnSelector_example.R
@@ -1,7 +1,7 @@
 library(shiny)
 source("../R/columnSelector.R")
 
-###Test Data
+### Test Data
 table <- data.table::data.table(id = c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j"), level = c("sample", "condition", "contrast"), sub_label = "sub")
 names(table)[1] <- "key"
 
@@ -27,22 +27,21 @@ type <- reactive({
   unique(table[[2]])[-1]
 })
 
-  mod <-callModule(columnSelector, "id", type.columns = table, multiple = FALSE, none = TRUE)
-  mod2 <-callModule(columnSelector, "2", type.columns = data, type = type)
+  mod <- callModule(columnSelector, "id", type.columns = table, multiple = FALSE, none = TRUE)
+  mod2 <- callModule(columnSelector, "2", type.columns = data, type = type)
 
   output$first <- renderPrint({
     print(mod$type())
-    print(mod$selectedColumn())
+    print(mod$selected_column())
     print(mod$label())
   })
 
   output$second <- renderPrint({
     print(mod2$type())
-    print(mod2$selectedColumn())
+    print(mod2$selected_column())
     print(mod2$label())
   })
 }
 
 # Run the application
 shinyApp(ui = ui, server = server)
-
diff --git a/man/columnSelector.Rd b/man/columnSelector.Rd
index 6cb7593..9ababef 100644
--- a/man/columnSelector.Rd
+++ b/man/columnSelector.Rd
@@ -5,7 +5,7 @@
 \title{columnSelector module server logic}
 \usage{
 columnSelector(input, output, session, type.columns, type = NULL,
-  columnTypeLabel = "Type of Column", labelLabel = "Label",
+  column.type.label = "Type of Column", label.label = "Label",
   multiple = TRUE, none = FALSE, sep = ", ", suffix = NULL)
 }
 \arguments{
@@ -23,9 +23,7 @@ sub_label = optional, added to id/ label}
 
 \item{type}{The type (contrast/group/sample of the type dropdown menu, selected in step 1 (upper dropdown). Defaults to unique(type.columns[,2]) (Supports reactive)}
 
-\item{columnTypeLabel}{Changes the label of the first UI element}
-
-\item{labelLabel}{Change label above label text input.}
+\item{label.label}{Change label above label text input.}
 
 \item{multiple}{Boolean value whether multiple values can be selected in second selector. (Default = TRUE)}
 
@@ -34,9 +32,11 @@ sub_label = optional, added to id/ label}
 \item{sep}{Used to separate labels on multi value selection.}
 
 \item{suffix}{Added to label only on multiple = FALSE (supports reactive). Also uses sep as separator.}
+
+\item{column.type.tabel}{Changes the label of the first UI element}
 }
 \value{
-Returns the input. As named list: names("type", "selectedColumns", "label")
+Returns the input. As named list: names("type", "selected_columns", "label")
 }
 \description{
 columnSelector module server logic

From b8334d5be46a110853aced19401919a51cdf25fd Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 09:31:16 +0200
Subject: [PATCH 48/75] lint clarion

---
 R/clarion.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/clarion.R b/R/clarion.R
index f9ebe6c..5c0260d 100644
--- a/R/clarion.R
+++ b/R/clarion.R
@@ -66,7 +66,7 @@ Clarion <- R6::R6Class("Clarion",
                            if (is.element("type", names(self$metadata)) && is.element("name", self$metadata[["type"]])) {
                              return(self$metadata[type == "name"][["key"]])
                            }
-                           return(self$get_uniqueid())
+                           return(self$get_id())
                          },
                          get_delimiter = function() {
                            self$header$delimiter

From 4de0a3818636a830c4bfa1c514e7cba72220cc8e Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 09:31:40 +0200
Subject: [PATCH 49/75] lint featureSelector

---
 R/featureSelector.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/featureSelector.R b/R/featureSelector.R
index 71425e9..2eea752 100644
--- a/R/featureSelector.R
+++ b/R/featureSelector.R
@@ -30,7 +30,7 @@ featureSelectorUI <- function(id){
                             shiny::actionButton(ns("guide"), "Launch guide", style = "color: #fff; background-color: #3c8dbc", icon = shiny::icon("question-circle")),
                             shiny::downloadButton(ns("download")),
                             shiny::br(),
-                            shiny::strong("NOTE: The SELECT button only evaluates the filter(s) below.",shiny::br(),
+                            shiny::strong("NOTE: The SELECT button only evaluates the filter(s) below.", shiny::br(),
                                           "Manual sub-selections on table applies instantly!", shiny::br(),
                                           "Repress of SELECT button discards manual selections!")
                             )
@@ -72,11 +72,11 @@ featureSelector <- function(input, output, session, clarion, multiple = TRUE, co
     if (shiny::is.reactive(clarion)) {
       if (!methods::is(clarion(), "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-      obj <- clarion()$clone(deep = TRUE)
+      clarion()$clone(deep = TRUE)
     } else {
       if (!methods::is(clarion, "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-      obj <- clarion$clone(deep = TRUE)
+      clarion$clone(deep = TRUE)
     }
   })
 
@@ -288,7 +288,7 @@ featureSelector <- function(input, output, session, clarion, multiple = TRUE, co
       }
 
       # create filter text
-      filter <- paste("Result:" , nrow(data), "hits")
+      filter <- paste("Result:", nrow(data), "hits")
     } else if (data_change() == 1) {
       data <- select()
 

From 7557b04fbef4b456fafd69c94d2675ab9b8334db Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 09:32:13 +0200
Subject: [PATCH 50/75] featureSelector: fixed wrong download var

---
 R/featureSelector.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/featureSelector.R b/R/featureSelector.R
index 2eea752..0e2be02 100644
--- a/R/featureSelector.R
+++ b/R/featureSelector.R
@@ -315,7 +315,7 @@ featureSelector <- function(input, output, session, clarion, multiple = TRUE, co
     content = function(file) {
       log_message("FeatureSelector: download", "INFO", token = session$token)
 
-      data.table::fwrite(x = result()$data, file = file, sep = "\t")
+      data.table::fwrite(x = result()$object$data, file = file, sep = "\t")
     }
   )
 

From 4c643919890425f2dc1a2f0ee3c97dbf8c61d3ee Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 10:27:54 +0200
Subject: [PATCH 51/75] lint function

---
 R/function.R          | 467 +++++++++++++++++++++---------------------
 man/create_heatmap.Rd |  11 +-
 man/create_pca.Rd     |   6 +-
 3 files changed, 241 insertions(+), 243 deletions(-)

diff --git a/R/function.R b/R/function.R
index 7cfbcd4..1aed7cf 100644
--- a/R/function.R
+++ b/R/function.R
@@ -57,19 +57,19 @@ create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL,
   if (ncol(data) >= 4) z_head <- names(data)[4]
 
   # delete rows where both 0 or at least one NA
-  rows.to.keep.data <- which(as.logical((data[, 2] != 0) + (data[, 3] != 0)))
-  data <- data[rows.to.keep.data]
+  rows_to_keep_data <- which(as.logical( (data[, 2] != 0) + (data[, 3] != 0)))
+  data <- data[rows_to_keep_data]
   if (!is.null(highlight.data)) {
-    rows.to.keep.high <- which(as.logical((highlight.data[, 2] != 0) + (highlight.data[, 3 != 0])))
-    highlight.data <- highlight.data[rows.to.keep.high]
+    rows_to_keep_high <- which(as.logical( (highlight.data[, 2] != 0) + (highlight.data[, 3 != 0])))
+    highlight.data <- highlight.data[rows_to_keep_high]
   }
 
   # delete labels & hovertext accordingly
-  data.labels <- data.labels[rows.to.keep.data]
-  data.hovertext <- data.hovertext[rows.to.keep.data]
+  data.labels <- data.labels[rows_to_keep_data]
+  data.hovertext <- data.hovertext[rows_to_keep_data]
   if (!is.null(highlight.data)) {
-    highlight.labels <- highlight.labels[rows.to.keep.high]
-    highlight.hovertext <- highlight.hovertext[rows.to.keep.high]
+    highlight.labels <- highlight.labels[rows_to_keep_high]
+    highlight.hovertext <- highlight.hovertext[rows_to_keep_high]
   }
 
   ########## assemble plot ##########
@@ -125,7 +125,7 @@ create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL,
   if (density) {
     ### kernel density
     # plot$layers <- c(stat_density2d(geom = "tile", aes(fill = ..density..^0.25), n=200, contour=FALSE) + aes_(fill = as.name(var)), plot$layers) # n = resolution; density less sparse
-    plot <- plot + ggplot2::stat_density2d(geom = "tile", ggplot2::aes_(fill = ~ ..density..^0.25), n = 200, contour = FALSE)
+    plot <- plot + ggplot2::stat_density2d(geom = "tile", ggplot2::aes_(fill = ~ ..density.. ^ 0.25), n = 200, contour = FALSE)
 
     plot <- plot + ggplot2::scale_fill_gradient(low = "white", high = "black") +
       # guides(fill=FALSE) +		# remove density legend
@@ -279,10 +279,10 @@ create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL,
 
     # add labels with arrows
     if (!is.null(highlight.labels) && !is.null(highlight.data)) {
-      plot <- plotly::add_annotations(p = plot, x = highlight.data[[x_head]], y = highlight.data[[y_head]], text = highlight.labels, standoff = pointsize * scale, font = list(size = labelsize * scale), bgcolor = 'rgba(255, 255, 255, 0.5)')
+      plot <- plotly::add_annotations(p = plot, x = highlight.data[[x_head]], y = highlight.data[[y_head]], text = highlight.labels, standoff = pointsize * scale, font = list(size = labelsize * scale), bgcolor = "rgba(255, 255, 255, 0.5)")
     }
     if (!is.null(data.labels)) {
-      plot <- plotly::add_annotations(p = plot, x = data[[x_head]], y = data[[y_head]], text = data.labels, standoff = pointsize * scale, font = list(size = labelsize * scale), bgcolor = 'rgba(255, 255, 255, 0.5)')
+      plot <- plotly::add_annotations(p = plot, x = data[[x_head]], y = data[[y_head]], text = data.labels, standoff = pointsize * scale, font = list(size = labelsize * scale), bgcolor = "rgba(255, 255, 255, 0.5)")
     }
   }
 
@@ -303,8 +303,8 @@ create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL,
 #' @param shape.group Vector of groups according to samples (= column names).
 #' @param shape.title Title of the shape legend.
 #' @param shapes Vector of shapes see \code{\link[graphics]{points}}. Will recycle/ cut off shapes if needed. Default = c(15:25)
-#' @param dimensionA Number of dimension displayed on X-Axis.
-#' @param dimensionB Number of dimension displayed on Y-Axis.
+#' @param dimension.a Number of dimension displayed on X-Axis.
+#' @param dimension.b Number of dimension displayed on Y-Axis.
 #' @param dimensions Number of dimensions to create.
 #' @param on.columns Boolean perform pca on columns or rows.
 #' @param labels Boolean show labels.
@@ -322,7 +322,7 @@ create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL,
 #' @import data.table
 #'
 #' @return A named list(plot = ggplot object, data = pca.data, width = width of plot (cm), height = height of plot (cm), ppi = pixel per inch, exceed_size = Boolean whether width/ height exceeded max).
-create_pca <- function(data, color.group = NULL, color.title = NULL, palette = NULL, shape.group = NULL, shape.title = NULL, shapes = c(15:25), dimensionA = 1, dimensionB = 2, dimensions = 6, on.columns = TRUE, labels = FALSE, custom.labels = NULL, pointsize = 2, labelsize = 3, width = 28, height = 28, ppi = 72, scale = 1) {
+create_pca <- function(data, color.group = NULL, color.title = NULL, palette = NULL, shape.group = NULL, shape.title = NULL, shapes = c(15:25), dimension.a = 1, dimension.b = 2, dimensions = 6, on.columns = TRUE, labels = FALSE, custom.labels = NULL, pointsize = 2, labelsize = 3, width = 28, height = 28, ppi = 72, scale = 1) {
   # force evaluation of all arguments
   # no promises in plot object
   forceArgs()
@@ -398,10 +398,10 @@ create_pca <- function(data, color.group = NULL, color.title = NULL, palette = N
   } else {
     invisible <-  "ind"
     # prepare df for mapping
-    df <- data.frame(x = pca$ind$coord[, dimensionA], y = pca$ind$coord[, dimensionB])
+    df <- data.frame(x = pca$ind$coord[, dimension.a], y = pca$ind$coord[, dimension.b])
   }
 
-  pca_plot <- factoextra::fviz_pca_ind(pca, axes = c(dimensionA, dimensionB), invisible = invisible, pointsize = pointsize * scale, label = "none", axes.linetype = "blank", repel = FALSE)
+  pca_plot <- factoextra::fviz_pca_ind(pca, axes = c(dimension.a, dimension.b), invisible = invisible, pointsize = pointsize * scale, label = "none", axes.linetype = "blank", repel = FALSE)
   pca_plot <- pca_plot + theme1
 
   # grouping
@@ -446,7 +446,7 @@ create_pca <- function(data, color.group = NULL, color.title = NULL, palette = N
   if (labels) {
     pca_plot <- pca_plot + ggrepel::geom_text_repel(
       data = data.frame(pca$ind$coord),
-      mapping = ggplot2::aes_(x = pca$ind$coord[, dimensionA], y = pca$ind$coord[, dimensionB], label = rownames(pca$ind$coord)),
+      mapping = ggplot2::aes_(x = pca$ind$coord[, dimension.a], y = pca$ind$coord[, dimension.b], label = rownames(pca$ind$coord)),
       segment.color = "gray65",
       size = labelsize * scale,
       force = 2,
@@ -500,7 +500,7 @@ create_pca <- function(data, color.group = NULL, color.title = NULL, palette = N
 #' @details Width/ height limit = 500. If exceeded default to 500 and issue exceed_size = TRUE.
 #'
 #' @return Returns list(plot = complexHeatmap/ plotly object, width = width in cm, height = height in cm, ppi = pixel per inch, exceed_size = Boolean whether width/ height exceeded max) depending on plot.method.
-create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label = NULL, column.label=T, column.custom.label = NULL, clustering='none', clustdist='auto', clustmethod='auto', colors=NULL, winsorize.colors = NULL, plot.method = "static", width = "auto", height = "auto", ppi = 72, scale = 1) {
+create_heatmap <- function(data, unitlabel = "auto", row.label = TRUE, row.custom.label = NULL, column.label = TRUE, column.custom.label = NULL, clustering = "none", clustdist = "auto", clustmethod = "auto", colors = NULL, winsorize.colors = NULL, plot.method = "static", width = "auto", height = "auto", ppi = 72, scale = 1) {
   # force evaluation of all arguments
   # no promises in plot object
   forceArgs()
@@ -510,55 +510,55 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
   requireNamespace("grDevices", quietly = TRUE)
   requireNamespace("circlize", quietly = TRUE)
 
-  #row label
-  if(!is.null(row.custom.label)) {
-    row.label.strings <- row.custom.label
+  # row label
+  if (!is.null(row.custom.label)) {
+    row_label_strings <- row.custom.label
   } else {
-    row.label.strings <- data[[1]]
+    row_label_strings <- data[[1]]
   }
 
   # column label
-  if(!is.null(column.custom.label)) {
-    column.label.strings <- column.custom.label
+  if (!is.null(column.custom.label)) {
+    column_label_strings <- column.custom.label
   } else {
-    column.label.strings <- names(data)[-1]
+    column_label_strings <- names(data)[-1]
   }
 
   # cm to pixel
-  if(is.numeric(width)) {
+  if (is.numeric(width)) {
     width <- width * (ppi / 2.54)
   }
-  if(is.numeric(height)) {
+  if (is.numeric(height)) {
     height <- height * (ppi / 2.54)
   }
 
   # plot --------------------------------------------------------------------
-  if(plot.method == "interactive"){
-    #estimate label sizes
-    #row label
+  if (plot.method == "interactive") {
+    # estimate label sizes
+    # row label
     rowlabel_size <- ifelse(row.label, max(nchar(data[[1]]), na.rm = TRUE) * 8 * scale, 0)
-    #column label
-    collabel_size <- ifelse(column.label, (2 + log2(max(nchar(names(data)), na.rm = TRUE))^2) * 10, 0)
-    #legend
+    # column label
+    collabel_size <- ifelse(column.label, (2 + log2(max(nchar(names(data)), na.rm = TRUE)) ^ 2) * 10, 0)
+    # legend
     legend <- nchar(unitlabel) * 10
     legend <- ifelse(legend < 90, 90, legend)
-    #plot size
-    #auto_width <- 20 * (ncol(data) - 1) + rowlabel_size + legend
+    # plot size
+    # auto_width <- 20 * (ncol(data) - 1) + rowlabel_size + legend
     auto_height <- 10 * nrow(data) + collabel_size
 
-    #data
+    # data
     plot <- heatmaply::heatmapr(data[, -1],
-                                labRow = row.label.strings,
-                                labCol = column.label.strings,
+                                labRow = row_label_strings,
+                                labCol = column_label_strings,
                                 hclust_method = clustmethod,
                                 dist_method = clustdist,
                                 dendrogram = clustering,
                                 distfun = factoextra::get_dist
-                                #width = width, #not working
-                                #height = height
+                                # width = width, #not working
+                                # height = height
     )
 
-    #layout
+    # layout
     plot <- heatmaply::heatmaply(plot,
                                  plot_method = "ggplot",
                                  node_type = "heatmap",
@@ -569,12 +569,12 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
     plot <- plotly::layout(plot, autosize = ifelse(width == "auto", TRUE, FALSE), margin = list(l = rowlabel_size, r = legend, b = collabel_size), showlegend = FALSE)
 
     # decide which sizes should be used
-    if(width == "auto") {
+    if (width == "auto") {
       width <- 0
     # } else if(width <= auto_width) {
     #   width <- auto_width
     }
-    if(height == "auto") {
+    if (height == "auto") {
       height <- auto_height
     }
 
@@ -585,11 +585,11 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
     # size exceeded?
     exceed_size <- FALSE
     limit <- 500 * (ppi / 2.54)
-    if(width > limit) {
+    if (width > limit) {
       exceed_size <- TRUE
       width <- limit
     }
-    if(height > limit) {
+    if (height > limit) {
       exceed_size <- TRUE
       height <- limit
     }
@@ -600,21 +600,21 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
     # address correct axis
     # scale axis tickfont
     ticks <- list(size = 12 * scale)
-    if(clustering == "both" || clustering == "column"){
+    if (clustering == "both" || clustering == "column") {
       plot <- plotly::layout(plot, xaxis = list(showticklabels = column.label, tickfont = ticks),
                              yaxis2 = list(showticklabels = row.label, tickfont = ticks)
       )
-    }else if(clustering == "row" || clustering == "none"){
+    }else if (clustering == "row" || clustering == "none") {
       plot <- plotly::layout(plot, xaxis = list(showticklabels = column.label, tickfont = ticks),
                              yaxis = list(showticklabels = row.label, tickfont = ticks)
       )
     }
 
-    #don't show dendrogram ticks
-    if(clustering == "row"){
+    # don't show dendrogram ticks
+    if (clustering == "row") {
       plot <- plotly::layout(plot, xaxis2 = list(showticklabels = FALSE)
       )
-    }else if(clustering == "column"){
+    }else if (clustering == "column") {
       plot <- plotly::layout(plot, yaxis = list(showticklabels = FALSE)
       )
     }
@@ -624,41 +624,41 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
     height <- height / (ppi / 2.54)
 
     plot <- list(plot = plot, width = width, height = height, ppi = ppi, exceed_size = exceed_size)
-  }else if(plot.method == "static"){
-
-    #clustering
-    if (clustering=='none') {
-      cluster_rows=F
-      cluster_columns=F
-    } else if (clustering=='row') {
-      cluster_rows=T
-      cluster_columns=F
-    } else if (clustering=='column') {
-      cluster_rows=F
-      cluster_columns=T
-    } else if (clustering=='both') {
-      cluster_rows=T
-      cluster_columns=T
+  }else if (plot.method == "static") {
+
+    # clustering
+    if (clustering == "none") {
+      cluster_rows <- FALSE
+      cluster_columns <- FALSE
+    } else if (clustering == "row") {
+      cluster_rows <- TRUE
+      cluster_columns <- FALSE
+    } else if (clustering == "column") {
+      cluster_rows <- FALSE
+      cluster_columns <- TRUE
+    } else if (clustering == "both") {
+      cluster_rows <- TRUE
+      cluster_columns <- TRUE
     }
 
     #
     # Create new colour brakepoints in case of winsorizing
     #
-    if(!is.null(winsorize.colors)) {
+    if (!is.null(winsorize.colors)) {
       breaks <- seq(winsorize.colors[1], winsorize.colors[2], length = length(colors))
     } else {
       breaks <- seq(min(apply(data[, -1], 2, function(x) {min(x, na.rm = TRUE)})), max(apply(data[, -1], 2, function(x) {max(x, na.rm = TRUE)})), length = length(colors))
     }
     colors <- circlize::colorRamp2(breaks, colors)
 
-    #convert data to data.frame so rownames can be used for annotation
-    prep.data <- as.data.frame(data[, -1])
+    # convert data to data.frame so rownames can be used for annotation
+    prep_data <- as.data.frame(data[, -1])
 
-    row.names(prep.data) <- row.label.strings
-    colnames(prep.data) <- column.label.strings
+    row.names(prep_data) <- row_label_strings
+    colnames(prep_data) <- column_label_strings
 
     plot <- try(ComplexHeatmap::Heatmap(
-      prep.data,
+      prep_data,
       name = unitlabel,
       col = colors,
       cluster_rows = cluster_rows,
@@ -689,40 +689,40 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
       )
     ))
 
-    #width/ height calculation
-    col_names_maxlength_label_width=max(sapply(colnames(prep.data), graphics::strwidth, units="in", font = 12))	#longest column label when plotted in inches
-    col_names_maxlength_label_height=max(sapply(colnames(prep.data), graphics::strheight, units="in", font = 12))	#highest column label when plotted in inches
-    row_names_maxlength_label_width=max(sapply(rownames(prep.data), graphics::strwidth, units="in", font = 12))	#longest row label when plotted in inches
-    row_names_maxlength_label_height=max(sapply(rownames(prep.data), graphics::strheight, units="in", font = 12))	#highest row label when plotted in inches
+    # width/ height calculation
+    col_names_maxlength_label_width <- max(sapply(colnames(prep_data), graphics::strwidth, units = "in", font = 12))	# longest column label when plotted in inches
+    col_names_maxlength_label_height <- max(sapply(colnames(prep_data), graphics::strheight, units = "in", font = 12))	# highest column label when plotted in inches
+    row_names_maxlength_label_width <- max(sapply(rownames(prep_data), graphics::strwidth, units = "in", font = 12))	# longest row label when plotted in inches
+    row_names_maxlength_label_height <- max(sapply(rownames(prep_data), graphics::strheight, units = "in", font = 12))	# highest row label when plotted in inches
 
     # width
-    if(row.label){
-      auto_width <- row_names_maxlength_label_width + 0.3 #width buffer: labels + small whitespaces
-    }else{
-      auto_width <- 0.3 #no labels
+    if (row.label) {
+      auto_width <- row_names_maxlength_label_width + 0.3 # width buffer: labels + small whitespaces
+    } else {
+      auto_width <- 0.3 # no labels
     }
 
-    if(cluster_rows) auto_width <- auto_width + 1 #width buffer: dendrogram + small whitespaces between viewports
+    if (cluster_rows) auto_width <- auto_width + 1 # width buffer: dendrogram + small whitespaces between viewports
 
-    auto_width <- ncol(prep.data) * (col_names_maxlength_label_height + 0.08) + auto_width #readable rowlabels
+    auto_width <- ncol(prep_data) * (col_names_maxlength_label_height + 0.08) + auto_width # readable rowlabels
     # inch to px
     auto_width <- auto_width * ppi
 
     # height
-    auto_height <- 0.2 + 0.5 + (5 * row_names_maxlength_label_height) #height buffer: small whitespaces + color legend + 2 title rows(+whitespace)
+    auto_height <- 0.2 + 0.5 + (5 * row_names_maxlength_label_height) # height buffer: small whitespaces + color legend + 2 title rows(+whitespace)
 
-    if(column.label) auto_height <- auto_height + col_names_maxlength_label_width
-    if(cluster_columns) auto_height <- auto_height + 1
+    if (column.label) auto_height <- auto_height + col_names_maxlength_label_width
+    if (cluster_columns) auto_height <- auto_height + 1
 
-    auto_height <- auto_height + nrow(prep.data) * (row_names_maxlength_label_height + 0.06)
+    auto_height <- auto_height + nrow(prep_data) * (row_names_maxlength_label_height + 0.06)
     # inch to px
     auto_height <- auto_height * ppi
 
     # use auto sizes
-    if(height == "auto") {
+    if (height == "auto") {
       height <- auto_height
     }
-    if(width == "auto") {
+    if (width == "auto") {
       width <- auto_width
     }
 
@@ -732,11 +732,11 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
 
     # size exceeded?
     exceed_size <- FALSE
-    if(width > 500) {
+    if (width > 500) {
       exceed_size <- TRUE
       width <- 500
     }
-    if(height > 500) {
+    if (height > 500) {
       exceed_size <- TRUE
       height <- 500
     }
@@ -775,18 +775,18 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
   # force evaluation of all arguments
   # no promises in plot object
   forceArgs()
-  #grouping
-  #group by factor if existing (fill with key if empty)
+  # grouping
+  # group by factor if existing (fill with key if empty)
   grouping[grouping[[2]] == "", 2 := grouping[grouping[[2]] == "", 1]]
 
-  genes <- nrow(data)												#number of genes (rows in matrix)
-  conditions <- length(unique(grouping[[2]]))											#number of conditions (columns in matrix)
+  genes <- nrow(data)												# number of genes (rows in matrix)
+  conditions <- length(unique(grouping[[2]]))											# number of conditions (columns in matrix)
 
   ###################
   # Combine and transform dataframes
   ###################
-  #detach ids from data/ replace with gene.label
-  if(is.null(gene.label)) {
+  # detach ids from data/ replace with gene.label
+  if (is.null(gene.label)) {
     data_id <- data[[1]]
   } else {
     data_id <- gene.label
@@ -794,19 +794,19 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
   data <- data[, sapply(data, is.numeric), with = FALSE]
 
   data_cols <- names(data)
-  data <- data.table::transpose(data) 								#switch columns <> rows
+  data <- data.table::transpose(data) 								# switch columns <> rows
 
-  #place former colnames in cols
+  # place former colnames in cols
   data$cols <- data_cols
-  data.table::setcolorder(data, c("cols", colnames(data)[1:ncol(data)-1]))
-  #reattach ids as colnames
+  data.table::setcolorder(data, c("cols", colnames(data)[1:ncol(data) - 1]))
+  # reattach ids as colnames
   names(data)[2:ncol(data)] <- data_id
 
-  names(grouping)[1:2] <- c("cols", "condition") #add header for condition
-  data <- data[grouping, on = c(names(grouping)[1])]					#merge dataframes by rownames
-  names(data)[1] <- "sample"							#change Row.names to sample
-  data[, sample := NULL]								#completely remove sample column again
-  #order conditions in plot according to grouping (instead of alphabetic)
+  names(grouping)[1:2] <- c("cols", "condition") # add header for condition
+  data <- data[grouping, on = c(names(grouping)[1])]					# merge dataframes by rownames
+  names(data)[1] <- "sample"							# change Row.names to sample
+  data[, sample := NULL]								# completely remove sample column again
+  # order conditions in plot according to grouping (instead of alphabetic)
   data[, condition := factor(condition, levels = unique(condition))]
 
   data <- data.table::melt(data, id.vars = "condition")
@@ -814,28 +814,28 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
   ###################
   # Choose color palette
   ###################
-  if (facet.target == "gene") {											#facet = gene
+  if (facet.target == "gene") {											# facet = gene
     num_colors <- conditions
   }
-  if (facet.target == "condition") {										#facet = condition
+  if (facet.target == "condition") {										# facet = condition
     num_colors <- genes
   }
 
 
   if (is.null(colors)) {
-    color_fill_grayscale="grey75"										#color to use for filling geoms in grayscale mode
-    colors <- rep(color_fill_grayscale,num_colors)
-  }else{
+    color_fill_grayscale <- "grey75"										#color to use for filling geoms in grayscale mode
+    colors <- rep(color_fill_grayscale, num_colors)
+  } else {
     colors <- grDevices::colorRampPalette(colors)(num_colors)
   }
 
   ###################
   # Function to get standard error for error bars (box, bar, violin)
   ###################
-  get.se <- function(y){
+  get.se <- function(y) {
     se <- stats::sd(y) / sqrt(length(y))
     mu <- mean(y)
-    data.frame(ymin = mu-se, y = y, ymax = mu+se)
+    data.frame(ymin = mu - se, y = y, ymax = mu + se)
   }
 
   ###################
@@ -845,20 +845,21 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
   # data : a data frame
   # varname : the name of a column containing the variable to be summarized
   # groupnames : vector of column names to be used as grouping variables
-  data_summary <- function(data, varname, groupnames){
-    summary_func <- function(x, col){
+  data_summary <- function(data, varname, groupnames) {
+    summary_func <- function(x, col) {
       c(
-        mean = mean(x[[col]], na.rm=TRUE),
-        sd = stats::sd(x[[col]], na.rm=TRUE),
-        se = stats::sd(x[[col]], na.rm=TRUE) / sqrt(length(x[[col]]))
+        mean = mean(x[[col]], na.rm = TRUE),
+        sd = stats::sd(x[[col]], na.rm = TRUE),
+        se = stats::sd(x[[col]], na.rm = TRUE) / sqrt(length(x[[col]]))
       )
     }
-    data_sum <- plyr::ddply(data, groupnames, .fun=summary_func, varname)
+    data_sum <- plyr::ddply(data, groupnames, .fun = summary_func, varname)
     data_sum <- reshape::rename(data_sum, c("mean" = varname))
     return(data_sum)
   }
+
   if (plot.type == "line") {
-    data = data_summary(data, varname = "value", groupnames = c("condition", "variable"))			#collapse the dataframe to the mean and the standard deviation for line plot
+    data <- data_summary(data, varname = "value", groupnames = c("condition", "variable"))			# collapse the dataframe to the mean and the standard deviation for line plot
   }
 
   if (plot.type == "box" || plot.type == "violin" || plot.type == "bar" || plot.type == "line") {
@@ -867,24 +868,22 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
     ###################
 
     # plot --------------------------------------------------------------------
-
-    theme1 <- ggplot2::theme(															#no gray background or helper lines
+    theme1 <- ggplot2::theme(															# no gray background or helper lines
       panel.grid.major = ggplot2::element_blank(),
       panel.grid.minor = ggplot2::element_blank(),
-      axis.text.x = ggplot2::element_text(angle = 90, hjust = 1, vjust = 1),										#x-axis sample lables = 90 degrees
+      axis.text.x = ggplot2::element_text(angle = 90, hjust = 1, vjust = 1),										# x-axis sample lables = 90 degrees
       strip.background = ggplot2::element_blank(),
       panel.border = ggplot2::element_rect(colour = "black"),
-      legend.position = "none",														#remove legend
+      legend.position = "none",														# remove legend
       legend.title = ggplot2::element_blank(),
       axis.title.x = ggplot2::element_blank(),
       text = ggplot2::element_text(family = "mono", size = 15 * scale)
-
-      #axis.line.x = element_line(size = .3),
-      #axis.line.y = element_line(size = .3),
-      #panel.background = element_blank(),
-      #axis.title.y = element_text(face = "bold", color = "black", size = 10),
-      #plot.title = element_text(face = "bold", color = "black", size = 12),
-      #axis.text.x = element_text(angle = 90, hjust = 1)											#x-axis sample lables = vertical
+      # axis.line.x = element_line(size = .3),
+      # axis.line.y = element_line(size = .3),
+      # panel.background = element_blank(),
+      # axis.title.y = element_text(face = "bold", color = "black", size = 10),
+      # plot.title = element_text(face = "bold", color = "black", size = 12),
+      # axis.text.x = element_text(angle = 90, hjust = 1)											# x-axis sample lables = vertical
     )
 
     matrixplot <- ggplot2::ggplot(data, ggplot2::aes(y = value))
@@ -900,30 +899,30 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
     # Handle facetting and special parameters for line plot (no facetting, etc.)
     ###################
 
-    if (facet.target == "gene") {														#facet = gene
-      matrixplot = matrixplot + ggplot2::aes(x = condition, fill = condition)
+    if (facet.target == "gene") {														# facet = gene
+      matrixplot <- matrixplot + ggplot2::aes(x = condition, fill = condition)
 
-      if (plot.type == "line") {													#line plot: no facetting, different size algorithm
+      if (plot.type == "line") {													# line plot: no facetting, different size algorithm
         matrixplot <- matrixplot + ggplot2::aes_(x = ~ variable, colour = ~ condition, group = ~ condition, fill = NULL)
-        matrixplot <- matrixplot + ggplot2::scale_x_discrete(expand = c(0.05, 0.05))								#expand to reduce the whitespace inside the plot (left/right)
+        matrixplot <- matrixplot + ggplot2::scale_x_discrete(expand = c(0.05, 0.05))								# expand to reduce the whitespace inside the plot (left/right)
       } else {
-        #compute number of rows to get facet.cols columns (works better with plotly)
+        # compute number of rows to get facet.cols columns (works better with plotly)
         rows <- ceiling(length(levels(data$variable)) / facet.cols)
 
-        matrixplot <- matrixplot + ggplot2::facet_wrap(~variable, nrow = rows, scales = "free_x")
+        matrixplot <- matrixplot + ggplot2::facet_wrap( ~ variable, nrow = rows, scales = "free_x")
       }
     }
-    if (facet.target == "condition") {													#facet = condition
+    if (facet.target == "condition") {													# facet = condition
       matrixplot <- matrixplot + ggplot2::aes_(x = ~ variable, fill = ~ variable)
 
-      if (plot.type == "line") {													#line plot: no facetting, different size algorithm
+      if (plot.type == "line") {													# line plot: no facetting, different size algorithm
         matrixplot <- matrixplot + ggplot2::aes_(x = ~ condition, colour = ~ variable, group = ~ variable, fill = NULL)
-        matrixplot <- matrixplot + ggplot2::scale_x_discrete(expand = c(0.05,0.05))								#expand to reduce the whitespace inside the plot (left/right)
+        matrixplot <- matrixplot + ggplot2::scale_x_discrete(expand = c(0.05, 0.05))								# expand to reduce the whitespace inside the plot (left/right)
       } else {
-        #compute number of rows to get facet.cols columns (works better with plotly)
+        # compute number of rows to get facet.cols columns (works better with plotly)
         rows <- ceiling(length(levels(data$condition)) / facet.cols)
 
-        matrixplot <- matrixplot + ggplot2::facet_wrap(~condition, nrow = rows, scales = "free_x")
+        matrixplot <- matrixplot + ggplot2::facet_wrap( ~ condition, nrow = rows, scales = "free_x")
       }
     }
 
@@ -931,26 +930,26 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
     # Further handle plot types
     ###################
 
-    if (plot.type == "box") {																#plot type: box
+    if (plot.type == "box") {																# plot type: box
       matrixplot <- matrixplot + ggplot2::geom_boxplot(position = ggplot2::position_dodge(1))
-      matrixplot <- matrixplot + ggplot2::stat_boxplot(geom = 'errorbar', size = 0.2, width = 0.5) 										#add horizontal line for errorbar
-      #matrixplot <- matrixplot + stat_summary(fun.data = get.se, geom = "errorbar", width = 0.2)					#error bar of standard error
+      matrixplot <- matrixplot + ggplot2::stat_boxplot(geom = "errorbar", size = 0.2, width = 0.5) 										# add horizontal line for errorbar
+      # matrixplot <- matrixplot + stat_summary(fun.data = get.se, geom = "errorbar", width = 0.2)					# error bar of standard error
     }
-    if (plot.type == "violin") {																#plot type: violin
+    if (plot.type == "violin") {																# plot type: violin
       matrixplot <- matrixplot + ggplot2::geom_violin()
-      #matrixplot <- matrixplot + stat_summary(fun.y = "median", geom = "point")										#add median dot
-      #matrixplot <- matrixplot + stat_summary(fun.data = get.se, geom = "errorbar", width = 0.2, position = position_dodge())					#error bar of standard error
+      # matrixplot <- matrixplot + stat_summary(fun.y = "median", geom = "point")										# add median dot
+      # matrixplot <- matrixplot + stat_summary(fun.data = get.se, geom = "errorbar", width = 0.2, position = position_dodge())					# error bar of standard error
     }
-    if (plot.type == "bar") {																#plot type: box
-      matrixplot <- matrixplot + ggplot2::stat_summary(fun.y = mean, geom = "bar", position = "dodge")							#bar plot of the mean (color=condition)
-      matrixplot <- matrixplot + ggplot2::stat_summary(fun.data = get.se, geom = "errorbar", size = 0.2, width = 0.2, position = ggplot2::position_dodge())					#error bar of standard error
+    if (plot.type == "bar") {																# plot type: box
+      matrixplot <- matrixplot + ggplot2::stat_summary(fun.y = mean, geom = "bar", position = "dodge")							# bar plot of the mean (color=condition)
+      matrixplot <- matrixplot + ggplot2::stat_summary(fun.data = get.se, geom = "errorbar", size = 0.2, width = 0.2, position = ggplot2::position_dodge())					# error bar of standard error
     }
     if (plot.type == "line") {
       matrixplot <- matrixplot + ggplot2::theme(legend.position = "right")
-      #matrixplot <- matrixplot + geom_errorbar(aes(ymin = value-sd, ymax = value + sd), width = 0.05)								#error bar = standard deviation
-      matrixplot <- matrixplot + ggplot2::geom_errorbar(ggplot2::aes_(ymin = ~ value - se, ymax = ~ value + se), size = 0.2, width = 0.05)								#error bar = standard error
-      matrixplot <- matrixplot + ggplot2::geom_line() + ggplot2::geom_point()											#bar plot of the mean (color=condition)
-      #set hovertext
+      # matrixplot <- matrixplot + geom_errorbar(aes(ymin = value - sd, ymax = value + sd), width = 0.05)								# error bar = standard deviation
+      matrixplot <- matrixplot + ggplot2::geom_errorbar(ggplot2::aes_(ymin = ~ value - se, ymax = ~ value + se), size = 0.2, width = 0.05)								# error bar = standard error
+      matrixplot <- matrixplot + ggplot2::geom_line() + ggplot2::geom_point()											# bar plot of the mean (color = condition)
+      # set hovertext
       matrixplot <- matrixplot + ggplot2::aes(text = paste("ID: ", data$variable, "\n",
                                                            "Condition: ", data$condition, "\n",
                                                            "Value: ", data$value
@@ -959,100 +958,99 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
 
     # set y-axis ticks
     y_ticks <- pretty(data[["value"]])
-    if(length(data[["value"]]) != 1) {
-      if(!is.null(ylimits)) {
+    if (length(data[["value"]]) != 1) {
+      if (!is.null(ylimits)) {
         y_ticks <- pretty(ylimits)
       }
 
       matrixplot <- matrixplot + ggplot2::scale_y_continuous(breaks = y_ticks, limits = ylimits)
     } else {
       # change yaxis limits
-      if(!is.null(ylimits)) {
+      if (!is.null(ylimits)) {
         matrixplot <- matrixplot + ggplot2::ylim(ylimits)
       }
     }
   }
 
-  #get names of columns / rows
-  if(plot.type == "line"){
-    if(facet.target == "gene"){
-      column.names <- data[["variable"]]
-      legend.names <- data[["condition"]]
-    }else{
-      column.names <- data[["condition"]]
-      legend.names <- data[["variable"]]
+  # get names of columns / rows
+  if (plot.type == "line") {
+    if (facet.target == "gene") {
+      column_names <- data[["variable"]]
+      legend_names <- data[["condition"]]
+    } else {
+      column_names <- data[["condition"]]
+      legend_names <- data[["variable"]]
     }
-  }else{
-    if(facet.target == "condition"){
-      column.names <- data[["variable"]]
-      title.names <- data[["condition"]]
-    }else{
-      column.names <- data[["condition"]]
-      title.names <- data[["variable"]]
+  } else {
+    if (facet.target == "condition") {
+      column_names <- data[["variable"]]
+      title_names <- data[["condition"]]
+    } else {
+      column_names <- data[["condition"]]
+      title_names <- data[["variable"]]
     }
   }
 
-  #dynamic plot in inches
-
-  #calculate cex for better strwidth calculation
+  # dynamic plot in inches
+  # calculate cex for better strwidth calculation
   ccex <- function(x){
-    2.3 - (x * log(1 + 1/x))
+    2.3 - (x * log(1 + 1 / x))
   }
 
-  ###width estimation
+  ### width estimation
   yaxis_label_height <- graphics::strheight(ylabel, units = "inches")
-  if(length(data[["value"]]) == 1 && floor(data[["value"]]) == data[["value"]]) {
+  if (length(data[["value"]]) == 1 && floor(data[["value"]]) == data[["value"]]) {
     # adds three characters '.05'; account for single integer value plots
     value <- data[["value"]] + 0.05
   } else {
     value <- y_ticks
   }
   yaxis_tick_width <- max(graphics::strwidth(value, units = "inches"), na.rm = TRUE)
-  xaxis_tick_height <- max(graphics::strheight(column.names, units = "inches", cex = 2), na.rm = TRUE) * length(levels(column.names))
-  ###height estimation
-  xaxis_tick_width <- max(graphics::strwidth(column.names, units = "inches", cex = ccex(max(nchar(levels(column.names))))), na.rm = TRUE)
+  xaxis_tick_height <- max(graphics::strheight(column_names, units = "inches", cex = 2), na.rm = TRUE) * length(levels(column_names))
+  ### height estimation
+  xaxis_tick_width <- max(graphics::strwidth(column_names, units = "inches", cex = ccex(max(nchar(levels(column_names))))), na.rm = TRUE)
 
-  if(plot.type == "line"){
-    ###width estimation
-    max_chars <- max(nchar(levels(legend.names)), na.rm = TRUE)
-    legend_width <- max(graphics::strwidth(legend.names, units = "inches", cex = ccex(max_chars)), na.rm = TRUE)
-    legend_columns <- 1 + (length(levels(legend.names))-1) %/% 20
+  if (plot.type == "line") {
+    ### width estimation
+    max_chars <- max(nchar(levels(legend_names)), na.rm = TRUE)
+    legend_width <- max(graphics::strwidth(legend_names, units = "inches", cex = ccex(max_chars)), na.rm = TRUE)
+    legend_columns <- 1 + (length(levels(legend_names)) - 1) %/% 20
 
-    auto_width <- 0.25 + yaxis_label_height + yaxis_tick_width + xaxis_tick_height + ((legend_width + 0.5) * legend_columns)
+    auto_width <- 0.25 + yaxis_label_height + yaxis_tick_width + xaxis_tick_height + (legend_width + 0.5) * legend_columns
 
-    ###height estimation
+    ### height estimation
     plot_height <- 4
 
-    #top margin to prevent legend cut off
+    # top margin to prevent legend cut off
     top <- 0
-    if(plot.method == "static"){
-      margin.multiplier <- ceiling(length(levels(legend.names)) / legend_columns)
-      margin.multiplier <- ifelse(margin.multiplier < 17, 0, margin.multiplier - 17)
+    if (plot.method == "static") {
+      margin_multiplier <- ceiling(length(levels(legend_names)) / legend_columns)
+      margin_multiplier <- ifelse(margin_multiplier < 17, 0, margin_multiplier - 17)
 
-      top <- 0.1 * margin.multiplier
+      top <- 0.1 * margin_multiplier
       matrixplot <- matrixplot + ggplot2::theme(plot.margin = grid::unit(c(top + 0.1, 0, 0, 0), "inches"))
     }
 
     auto_height <- plot_height + xaxis_tick_width + top
-  }else{
-    ###width estimation
-    max_chars <- max(nchar(levels(title.names)), na.rm = TRUE)
+  } else {
+    ### width estimation
+    max_chars <- max(nchar(levels(title_names)), na.rm = TRUE)
 
-    title_width <- max(graphics::strwidth(title.names, units = "inches", cex = ccex(max_chars)), na.rm = TRUE)
+    title_width <- max(graphics::strwidth(title_names, units = "inches", cex = ccex(max_chars)), na.rm = TRUE)
     # prevent cut off for small titles
-    title.chars <- sum(nchar(levels(title.names)))
-    if(facet.cols == 1 && max(nchar(levels(title.names))) <= 20) {
-        title_width <- title_width + (-log10(max(nchar(levels(title.names)))) + 1.6) / 3
-    } else if(title.chars <= 20) {
-      title_width <- title_width + (-log10(title.chars) + 1.4) / 3
+    title_chars <- sum(nchar(levels(title_names)))
+    if (facet.cols == 1 && max(nchar(levels(title_names))) <= 20) {
+        title_width <- title_width + (-log10(max(nchar(levels(title_names)))) + 1.6) / 3
+    } else if (title_chars <= 20) {
+      title_width <- title_width + (-log10(title_chars) + 1.4) / 3
     }
-    #TODO margin between plots (not really needed)
-    plots_per_row <- ceiling(length(levels(title.names))/ rows)
+    # TODO margin between plots (not really needed)
+    plots_per_row <- ceiling(length(levels(title_names)) / rows)
 
     auto_width <- yaxis_label_height + yaxis_tick_width + (ifelse(title_width > xaxis_tick_height, title_width, xaxis_tick_height) * plots_per_row)
 
     ###height estimation
-    title_height <- max(graphics::strheight(title.names, units = "inches", cex = 2), na.rm = TRUE)
+    title_height <- max(graphics::strheight(title_names, units = "inches", cex = 2), na.rm = TRUE)
     plot_height <- 2
 
 
@@ -1064,10 +1062,10 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
   auto_height <- auto_height * 2.54
 
   # use greater/ automatic sizes
-  if(width == "auto") {
+  if (width == "auto") {
     width <- auto_width
   }
-  if(height == "auto") {
+  if (height == "auto") {
     height <- auto_height
   }
 
@@ -1077,17 +1075,17 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
 
   # size exceeded?
   exceed_size <- FALSE
-  if(width > 500) {
+  if (width > 500) {
     exceed_size <- TRUE
     width <- 500
   }
-  if(height > 500) {
+  if (height > 500) {
     exceed_size <- TRUE
     height <- 500
   }
 
   # plotly ------------------------------------------------------------------
-  if(plot.method == "interactive"){
+  if (plot.method == "interactive") {
     matrixplotly <- plotly::ggplotly(
       tooltip = "text",
       matrixplot,
@@ -1108,18 +1106,18 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
 #' @param values Numeric vector or table
 #'
 #' @return Vector with c(min, max).
-equalize <- function(values){
-  if(is.vector(values)){
+equalize <- function(values) {
+  if (is.vector(values)) {
     min <- abs(min(values, na.rm = TRUE))
     max <- abs(max(values, na.rm = TRUE))
-  }else{
+  } else {
     min <- abs(min(apply(values, 2, function(x) {min(x, na.rm = TRUE)})))
     max <- abs(max(apply(values, 2, function(x) {max(x, na.rm = TRUE)})))
   }
 
-  if(min > max){
+  if (min > max) {
     result <- min
-  }else{
+  } else {
     result <- max
   }
 
@@ -1136,49 +1134,49 @@ equalize <- function(values){
 #'
 #' @return Returns a logical vector with the length of choices, where every matched position is TRUE.
 searchData <- function(input, choices, options = c("=", "<", ">"), min. = min(choices, na.rm = TRUE), max. = max(choices, na.rm = TRUE)) {
-  #don't apply if no options selected
-  if(is.null(options)){
+  # don't apply if no options selected
+  if (is.null(options)) {
     return(rep(TRUE, length(choices)))
   }
 
-  if(length(input) > 1){
-    #don't compare if everything is selected
-    if(options == "inner" & input[1] == min. & input[2] == max.){
+  if (length(input) > 1) {
+    # don't compare if everything is selected
+    if (options == "inner" & input[1] == min. & input[2] == max.) {
       return(rep(TRUE, length(choices)))
     }
 
     selection <- vapply(choices, FUN.VALUE = logical(1), function(x) {
       # NA & NaN == FALSE
-      if(is.na(x) | is.nan(x)){
+      if (is.na(x) | is.nan(x)) {
         return(FALSE)
       }
 
-      #range
-      if("inner" == options){
-        if(x >= input[1] & x <= input[2]) return(TRUE)
+      # range
+      if ("inner" == options){
+        if (x >= input[1] & x <= input[2]) return(TRUE)
       }
-      if("outer" == options){
-        if(x < input[1] | x > input[2]) return(TRUE)
+      if ("outer" == options) {
+        if (x < input[1] | x > input[2]) return(TRUE)
       }
 
       return(FALSE)
     })
-  }else{
+  } else {
     selection <- vapply(choices, FUN.VALUE = logical(1), function(x) {
       # NA & NaN == FALSE
-      if(is.na(x) | is.nan(x)){
+      if (is.na(x) | is.nan(x)) {
         return(FALSE)
       }
 
       #single point
-      if(any("=" == options)){
-        if(x == input) return(TRUE)
+      if (any("=" == options)) {
+        if (x == input) return(TRUE)
       }
-      if(any("<" == options)){
-        if(x < input) return(TRUE)
+      if (any("<" == options)) {
+        if (x < input) return(TRUE)
       }
-      if(any(">" == options)){
-        if(x > input) return(TRUE)
+      if (any(">" == options)) {
+        if (x > input) return(TRUE)
       }
 
       return(FALSE)
@@ -1230,7 +1228,6 @@ download <- function(file, filename, plot, width, height, ppi = 72, save_plot =
   # save plots depending on given plot object
   if (ggplot2::is.ggplot(plot)) {
     # ggplot
-
     ggplot2::ggsave(plot_file_pdf, plot = plot, width = width, height = height, units = "cm", device = "pdf", useDingbats = FALSE)
     ggplot2::ggsave(plot_file_png, plot = plot, width = width, height = height, units = "cm", device = "png", dpi = ppi)
   } else if (class(plot)[1] == "plotly") {
diff --git a/man/create_heatmap.Rd b/man/create_heatmap.Rd
index c425135..4686f1f 100644
--- a/man/create_heatmap.Rd
+++ b/man/create_heatmap.Rd
@@ -4,11 +4,12 @@
 \alias{create_heatmap}
 \title{Method for heatmap creation}
 \usage{
-create_heatmap(data, unitlabel = "auto", row.label = T,
-  row.custom.label = NULL, column.label = T, column.custom.label = NULL,
-  clustering = "none", clustdist = "auto", clustmethod = "auto",
-  colors = NULL, winsorize.colors = NULL, plot.method = "static",
-  width = "auto", height = "auto", ppi = 72, scale = 1)
+create_heatmap(data, unitlabel = "auto", row.label = TRUE,
+  row.custom.label = NULL, column.label = TRUE,
+  column.custom.label = NULL, clustering = "none", clustdist = "auto",
+  clustmethod = "auto", colors = NULL, winsorize.colors = NULL,
+  plot.method = "static", width = "auto", height = "auto", ppi = 72,
+  scale = 1)
 }
 \arguments{
 \item{data}{data.table containing plot data. First column contains row labels.}
diff --git a/man/create_pca.Rd b/man/create_pca.Rd
index a0da5f8..4426b10 100644
--- a/man/create_pca.Rd
+++ b/man/create_pca.Rd
@@ -6,7 +6,7 @@
 \usage{
 create_pca(data, color.group = NULL, color.title = NULL, palette = NULL,
   shape.group = NULL, shape.title = NULL, shapes = c(15:25),
-  dimensionA = 1, dimensionB = 2, dimensions = 6, on.columns = TRUE,
+  dimension.a = 1, dimension.b = 2, dimensions = 6, on.columns = TRUE,
   labels = FALSE, custom.labels = NULL, pointsize = 2, labelsize = 3,
   width = 28, height = 28, ppi = 72, scale = 1)
 }
@@ -25,9 +25,9 @@ create_pca(data, color.group = NULL, color.title = NULL, palette = NULL,
 
 \item{shapes}{Vector of shapes see \code{\link[graphics]{points}}. Will recycle/ cut off shapes if needed. Default = c(15:25)}
 
-\item{dimensionA}{Number of dimension displayed on X-Axis.}
+\item{dimension.a}{Number of dimension displayed on X-Axis.}
 
-\item{dimensionB}{Number of dimension displayed on Y-Axis.}
+\item{dimension.b}{Number of dimension displayed on Y-Axis.}
 
 \item{dimensions}{Number of dimensions to create.}
 

From 8d6cb761173775410472e7f4b37663917b752f21 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 10:53:29 +0200
Subject: [PATCH 52/75] lint geneView

---
 R/geneView.R | 74 ++++++++++++++++++++++++++--------------------------
 1 file changed, 37 insertions(+), 37 deletions(-)

diff --git a/R/geneView.R b/R/geneView.R
index d8f391b..f33dfad 100644
--- a/R/geneView.R
+++ b/R/geneView.R
@@ -46,7 +46,7 @@ geneViewUI <- function(id, plot.columns = 3){
             shiny::column(
               width = 3,
               shiny::div(id = ns("guide_type"),
-                         shiny::selectInput(ns("plotType"), label = "Type of Plot", choices = c("box", "line", "violin", "bar"), selected = "line")),
+                         shiny::selectInput(ns("plot_type"), label = "Type of Plot", choices = c("box", "line", "violin", "bar"), selected = "line")),
               shiny::div(id = ns("guide_transformation"),
                          transformationUI(id = ns("transform"), choices = list(`None` = "raw", `log2` = "log2", `-log2` = "-log2", `log10` = "log10", `-log10` = "-log10", `Z score` = "zscore")),
                          shiny::textInput(ns("label"), label = "Y-Axis Label")),
@@ -58,7 +58,7 @@ geneViewUI <- function(id, plot.columns = 3){
               shiny::div(id = ns("guide_color"),
                          colorPickerUI(id = ns("color"), show.transparency = FALSE, show.scaleoptions = FALSE)),
               shiny::div(id = ns("guide_plotColumns"),
-                         shiny::sliderInput(ns("plotColumns"), label = "Plot Columns", min = 1, max = 7, value = plot.columns, step = 1))
+                         shiny::sliderInput(ns("plot_columns"), label = "Plot Columns", min = 1, max = 7, value = plot.columns, step = 1))
             )
           ),
           shiny::fluidRow(
@@ -100,7 +100,7 @@ geneViewUI <- function(id, plot.columns = 3){
 #' @export
 geneView <- function(input, output, session, clarion, plot.method = "static", label.sep = ", ", width = "auto", height = "auto", ppi = 72, scale = 1){
   # globals/ initialization #####
-  clearPlot <- shiny::reactiveVal(FALSE)
+  clear_plot <- shiny::reactiveVal(FALSE)
   # disable downloadButton on init
   shinyjs::disable("download")
 
@@ -110,11 +110,11 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
     if (shiny::is.reactive(clarion)) {
       if (!methods::is(clarion(), "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-      obj <- clarion()$clone(deep = TRUE)
+      clarion()$clone(deep = TRUE)
     } else {
       if (!methods::is(clarion, "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-      obj <- clarion$clone(deep = TRUE)
+      clarion$clone(deep = TRUE)
     }
   })
 
@@ -142,11 +142,11 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
   })
 
   # modules/ ui #####
-  colorPicker <- shiny::callModule(colorPicker, "color", distribution = "all", selected = "Dark2")
-  transform <- shiny::callModule(transformation, "transform", shiny::reactive(as.matrix(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes), selector$selectedColumns(), with = FALSE])))
-  selector <- shiny::callModule(columnSelector, "selector", type.columns = shiny::reactive(object()$metadata[level != "feature", c("key", "level")]), columnTypeLabel = "Select Columns")
+  color <- shiny::callModule(colorPicker, "color", distribution = "all", selected = "Dark2")
+  transform <- shiny::callModule(transformation, "transform", shiny::reactive(as.matrix(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes), selector$selected_columns(), with = FALSE])))
+  selector <- shiny::callModule(columnSelector, "selector", type.columns = shiny::reactive(object()$metadata[level != "feature", c("key", "level")]), column.type.label = "Select Columns")
   custom_label <- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes)]), sep = label.sep)
-  factor_data <- shiny::callModule(label, "group", label = "Select grouping factors", data = shiny::reactive(object()$get_factors()[key %in% selector$selectedColumns(), !"key"]), sep = label.sep, unique = FALSE)
+  factor_data <- shiny::callModule(label, "group", label = "Select grouping factors", data = shiny::reactive(object()$get_factors()[key %in% selector$selected_columns(), !"key"]), sep = label.sep, unique = FALSE)
   limiter <- shiny::callModule(limit, "limit", lower = shiny::reactive(get_limits()[1]), upper = shiny::reactive(get_limits()[2]))
 
   output$genes <- shiny::renderUI({
@@ -178,26 +178,26 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
     log_message("GeneView: reset", "INFO", token = session$token)
 
     shinyjs::reset("genes")
-    shinyjs::reset("plotType")
+    shinyjs::reset("plot_type")
     shinyjs::reset("groupby")
-    shinyjs::reset("plotColumns")
-    colorPicker <<- shiny::callModule(colorPicker, "color", distribution = "all", selected = "Dark2")
-    transform <<- shiny::callModule(transformation, "transform", shiny::reactive(as.matrix(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes), selector$selectedColumns(), with = FALSE])))
-    selector <<- shiny::callModule(columnSelector, "selector", type.columns = shiny::reactive(object()$metadata[level != "feature", c("key", "level")]), columnTypeLabel = "Select Columns")
+    shinyjs::reset("plot_columns")
+    color <<- shiny::callModule(colorPicker, "color", distribution = "all", selected = "Dark2")
+    transform <<- shiny::callModule(transformation, "transform", shiny::reactive(as.matrix(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes), selector$selected_columns(), with = FALSE])))
+    selector <<- shiny::callModule(columnSelector, "selector", type.columns = shiny::reactive(object()$metadata[level != "feature", c("key", "level")]), column.type.label = "Select Columns")
     custom_label <<- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes)]), sep = label.sep)
-    factor_data <<- shiny::callModule(label, "group", label = "Select grouping factors", data = shiny::reactive(object()$get_factors()[key %in% selector$selectedColumns(), !"key"]), sep = label.sep, unique = FALSE)
+    factor_data <<- shiny::callModule(label, "group", label = "Select grouping factors", data = shiny::reactive(object()$get_factors()[key %in% selector$selected_columns(), !"key"]), sep = label.sep, unique = FALSE)
     limiter <<- shiny::callModule(limit, "limit", lower = shiny::reactive(get_limits()[1]), upper = shiny::reactive(get_limits()[2]))
-    clearPlot(TRUE)
+    clear_plot(TRUE)
   })
 
   get_limits <- shiny::reactive({
-    equalize(result.data()$data[, c(-1, -2)])
+    equalize(result_data()$data[, c(-1, -2)])
   })
 
-  result.data <- shiny::eventReactive(input$plot, {
-    columns <- switch((object()$get_uniqueID() == object()$get_name()) + 1,
-                      c(object()$get_uniqueID(), object()$get_name()),
-                      object()$get_uniqueID())
+  result_data <- shiny::eventReactive(input$plot, {
+    columns <- switch((object()$get_id() == object()$get_name()) + 1,
+                      c(object()$get_id(), object()$get_name()),
+                      object()$get_id())
 
     result <- data.table::data.table(object()$data[which(object()$data[[object()$get_name()]] %in% input$genes), columns, with = FALSE], data.table::as.data.table(transform$data()))
 
@@ -211,7 +211,7 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
 
     # enable downloadButton
     shinyjs::enable("download")
-    clearPlot(FALSE)
+    clear_plot(FALSE)
 
     # new progress indicator
     progress <- shiny::Progress$new()
@@ -226,18 +226,18 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
     } else {
       factor <- factor_data()$label
     }
-    grouping <- data.table::data.table(object()$metadata[key %in% selector$selectedColumns(), key], factor)
+    grouping <- data.table::data.table(object()$metadata[key %in% selector$selected_columns(), key], factor)
 
     # plot
     plot <- create_geneview(
-      data = if (object()$get_uniqueID() == object()$get_name()) result.data()$data else result.data()$data[, -2], # without name column
+      data = if (object()$get_id() == object()$get_name()) result_data()$data else result_data()$data[, -2], # without name column
       grouping = grouping,
-      plot.type = input$plotType,
+      plot.type = input$plot_type,
       facet.target = input$groupby,
-      facet.cols = input$plotColumns,
-      colors = colorPicker()$palette,
+      facet.cols = input$plot_columns,
+      colors = color()$palette,
       ylabel = input$label,
-      gene.label = result.data()$label,
+      gene.label = result_data()$label,
       ylimits = unlist(unname(limiter())),
       plot.method = plot.method,
       width = size()$width,
@@ -254,7 +254,7 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
   # render plot ######
   if (plot.method == "interactive") {
     output$interactive <- plotly::renderPlotly({
-      if (clearPlot()) {
+      if (clear_plot()) {
         return()
       } else {
         log_message("GeneView: render plot interactive", "INFO", token = session$token)
@@ -275,7 +275,7 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
       width = shiny::reactive(plot()$width * (plot()$ppi / 2.54)),
       height = shiny::reactive(plot()$height * (plot()$ppi / 2.54)),
       {
-        if (clearPlot()) {
+        if (clear_plot()) {
           return()
         } else {
           log_message("GeneView: render plot static", "INFO", token = session$token)
@@ -306,7 +306,7 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
     # format data
     data <- list(
       genes = input$genes,
-      columns = list(type = selector$type(), selectedColumns = selector$selectedColumns()),
+      columns = list(type = selector$type(), selectedColumns = selector$selected_columns()),
       group = factor_data()$selected,
       groupby = input$groupby
     )
@@ -314,12 +314,12 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
     # format options
     label <- custom_label()$selected
     options <- list(
-      plot_type = input$plotType,
+      plot_type = input$plot_type,
       transformation = transform$method(),
       yaxis_label = input$label,
       yaxis_limit = limiter(),
-      plot_column = input$plotColumns,
-      colors = list(scheme = colorPicker()$name, reverse = colorPicker()$reverse),
+      plot_column = input$plot_columns,
+      colors = list(scheme = color()$name, reverse = color()$reverse),
       custom_label = label
     )
 
@@ -330,10 +330,10 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
   # notifications #####
   # enable plot button only if plot possible
   shiny::observe({
-    if (is.null(input$genes) || !shiny::isTruthy(selector$selectedColumns())) {
+    if (is.null(input$genes) || !shiny::isTruthy(selector$selected_columns())) {
       shiny::removeNotification(session$ns("violin"))
       shinyjs::disable("plot")
-    }else if (input$plotType == "violin") {
+    } else if (input$plot_type == "violin") {
       factor_levels <- table(droplevels(as.factor(factor_data()$label), exclude = ""))
 
       if (input$groupby == "condition") {
@@ -406,7 +406,7 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
     rintrojs::introjs(session, options = list(steps = guide()))
   })
 
-  return(shiny::reactive(result.data()$data))
+  return(shiny::reactive(result_data()$data))
 }
 
 #' geneView module guide

From bd79fb813e2d55369c8ff7276c2e7d02f14cfc62 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 10:55:02 +0200
Subject: [PATCH 53/75] lint global

---
 R/global.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/global.R b/R/global.R
index d5ae871..75aea44 100644
--- a/R/global.R
+++ b/R/global.R
@@ -11,7 +11,7 @@ wilson.globals <- new.env(parent = emptyenv())
 #'
 #' @export
 set_logger <- function(logger, token = NULL) {
-  if(is.null(logger) || methods::is(logger, "logger")) {
+  if (is.null(logger) || methods::is(logger, "logger")) {
     assign(x = paste0("logger", token), value = logger, envir = wilson.globals)
   }
 }
@@ -25,7 +25,7 @@ set_logger <- function(logger, token = NULL) {
 #' @details Does nothing if logger doesn't exist.
 #'
 log_message <- function(message, level = c("DEBUG", "INFO", "WARN", "ERROR", "FATAL"), token = NULL) {
-  if(exists(paste0("logger", token), envir = wilson.globals)) {
+  if (exists(paste0("logger", token), envir = wilson.globals)) {
     logger <- get(paste0("logger", token), envir = wilson.globals)
 
     switch(level,

From 0adf557f5d6f1d11f31bf0c020bbc4815b5c0f14 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 11:06:17 +0200
Subject: [PATCH 54/75] lint geneView

---
 R/geneView.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/geneView.R b/R/geneView.R
index f33dfad..72aead3 100644
--- a/R/geneView.R
+++ b/R/geneView.R
@@ -324,7 +324,7 @@ geneView <- function(input, output, session, clarion, plot.method = "static", la
     )
 
     # merge all
-    all <- list(data = data, options = options)
+    list(data = data, options = options)
   })
 
   # notifications #####

From f0abc10b4c732c3fc65e8e750cc2b68c4ffd4362 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 11:06:44 +0200
Subject: [PATCH 55/75] lint global_cor_heatmap

---
 R/global_cor_heatmap.R | 42 +++++++++++++++++++++---------------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/R/global_cor_heatmap.R b/R/global_cor_heatmap.R
index dc1dda4..77292d7 100644
--- a/R/global_cor_heatmap.R
+++ b/R/global_cor_heatmap.R
@@ -160,7 +160,7 @@ global_cor_heatmapUI <- function(id) {
 global_cor_heatmap <- function(input, output, session, clarion, plot.method = "static", width = "auto", height = "auto", ppi = 72, scale = 1) {
   # globals -----------------------------------------------------------------
   # clear plot
-  clearPlot <- shiny::reactiveVal(FALSE)
+  clear_plot <- shiny::reactiveVal(FALSE)
   # disable downloadButton on init
   shinyjs::disable("download")
 
@@ -170,11 +170,11 @@ global_cor_heatmap <- function(input, output, session, clarion, plot.method = "s
     if (shiny::is.reactive(clarion)) {
       if (!methods::is(clarion(), "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-      obj <- clarion()$clone(deep = TRUE)
+      clarion()$clone(deep = TRUE)
     } else {
       if (!methods::is(clarion, "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-      obj <- clarion$clone(deep = TRUE)
+      clarion$clone(deep = TRUE)
     }
   })
 
@@ -206,9 +206,9 @@ global_cor_heatmap <- function(input, output, session, clarion, plot.method = "s
   })
 
   # load internal modules
-  columns <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
-  transform <- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selectedColumns(), with = FALSE])))
-  colorPicker <- shiny::callModule(colorPicker, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(result_data()[, -1])))
+  columns <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), column.type.label = "Column types to choose from")
+  transform <- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selected_columns(), with = FALSE])))
+  color <- shiny::callModule(colorPicker, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(result_data()[, -1])))
 
   # load dynamic ui
   if (plot.method == "static") {
@@ -234,10 +234,10 @@ global_cor_heatmap <- function(input, output, session, clarion, plot.method = "s
     shinyjs::reset("label")
     shinyjs::reset("row_label")
     shinyjs::reset("column_label")
-    columns <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
-    transform <<- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selectedColumns(), with = FALSE])))
-    colorPicker <<- shiny::callModule(colorPicker, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(result_data()[, -1])))
-    clearPlot(TRUE)
+    columns <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), column.type.label = "Column types to choose from")
+    transform <<- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selected_columns(), with = FALSE])))
+    color <<- shiny::callModule(colorPicker, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(result_data()[, -1])))
+    clear_plot(TRUE)
   })
 
   # warning if plot size exceeds limits
@@ -261,9 +261,9 @@ global_cor_heatmap <- function(input, output, session, clarion, plot.method = "s
 
   # show warning if not enough columns selected
   shiny::observe({
-    shiny::req(columns$selectedColumns())
+    shiny::req(columns$selected_columns())
 
-    if (length(columns$selectedColumns()) < 2) {
+    if (length(columns$selected_columns()) < 2) {
       shiny::showNotification(
         ui = "Warning! At least two columns needed. Please select more.",
         id = session$ns("less_data_warning"),
@@ -276,7 +276,7 @@ global_cor_heatmap <- function(input, output, session, clarion, plot.method = "s
 
   # enable/ disable plot button
   shiny::observe({
-    if (!shiny::isTruthy(columns$selectedColumns()) || length(columns$selectedColumns()) < 2) {
+    if (!shiny::isTruthy(columns$selected_columns()) || length(columns$selected_columns()) < 2) {
       shinyjs::disable("plot")
     }else {
       shinyjs::enable("plot")
@@ -326,7 +326,7 @@ global_cor_heatmap <- function(input, output, session, clarion, plot.method = "s
     # enable downloadButton
     shinyjs::enable("download")
     # show plot
-    clearPlot(FALSE)
+    clear_plot(FALSE)
 
     # progress indicator
     progress <- shiny::Progress$new()
@@ -360,12 +360,12 @@ global_cor_heatmap <- function(input, output, session, clarion, plot.method = "s
       clustering = "both",
       clustdist = input$distance,
       clustmethod = input$method,
-      colors = colorPicker()$palette,
+      colors = color()$palette,
       width = size()$width,
       height = size()$height,
       ppi = size()$ppi,
       plot.method = plot.method,
-      winsorize.colors = colorPicker()$winsorize,
+      winsorize.colors = color()$winsorize,
       scale = size()$scale
     )
 
@@ -382,7 +382,7 @@ global_cor_heatmap <- function(input, output, session, clarion, plot.method = "s
       width = shiny::reactive(plot()$width * (plot()$ppi / 2.54)),
       height = shiny::reactive(plot()$height * (plot()$ppi / 2.54)),
       {
-        if (clearPlot()) {
+        if (clear_plot()) {
           return()
         } else {
           log_message("Global correlation heatmap: render plot static", "INFO", token = session$token)
@@ -405,7 +405,7 @@ global_cor_heatmap <- function(input, output, session, clarion, plot.method = "s
     )
   } else if (plot.method == "interactive") {
     output$interactive <- plotly::renderPlotly({
-      if (clearPlot()) {
+      if (clear_plot()) {
         return()
       } else {
         log_message("Global correlation heatmap: render plot interactive", "INFO", token = session$token)
@@ -434,7 +434,7 @@ global_cor_heatmap <- function(input, output, session, clarion, plot.method = "s
 
   user_input <- shiny::reactive({
     # format selection
-    selection <- list(type = columns$type(), selectedColumns = columns$selectedColumns())
+    selection <- list(type = columns$type(), selected_columns = columns$selected_columns())
 
     # format calculation
     calculation <- list(
@@ -451,14 +451,14 @@ global_cor_heatmap <- function(input, output, session, clarion, plot.method = "s
     # format options
     options <- list(
       transformation = transform$method(),
-      color = list(distribution = input$distribution, scheme = colorPicker()$name, reverse = colorPicker()$reverse, winsorize = colorPicker()$winsorize),
+      color = list(distribution = input$distribution, scheme = color()$name, reverse = color()$reverse, winsorize = color()$winsorize),
       unit_label = input$label,
       row_label = input$row_label,
       column_label = input$column_label
     )
 
     # merge all
-    all <- list(selection = selection, calculation = calculation, clustering = clustering, options = options)
+    list(selection = selection, calculation = calculation, clustering = clustering, options = options)
   })
 
   # return plotting data

From e662c4445c86742186ce2880713c91fd9e4d4615 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 11:17:18 +0200
Subject: [PATCH 56/75] lint heatmap

---
 R/heatmap.R | 92 ++++++++++++++++++++++++++---------------------------
 1 file changed, 46 insertions(+), 46 deletions(-)

diff --git a/R/heatmap.R b/R/heatmap.R
index c6b4759..a5d3646 100644
--- a/R/heatmap.R
+++ b/R/heatmap.R
@@ -34,13 +34,13 @@ heatmapUI <- function(id, row.label = TRUE) {
                          multiple = FALSE
                        ),
                        shiny::selectInput(
-                         ns("cluster.distance"),
+                         ns("cluster_distance"),
                          label = "Cluster distance",
                          choices = c("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski", "pearson", "spearman", "kendall"),
                          multiple = FALSE
                        ),
                        shiny::selectInput(
-                         ns("cluster.method"),
+                         ns("cluster_method"),
                          label = "Cluster method",
                          choices = c("average", "ward.D", "ward.D2", "single", "complete", "mcquitty"),
                          multiple = FALSE))
@@ -64,9 +64,9 @@ heatmapUI <- function(id, row.label = TRUE) {
             width = 3,
             shiny::div(id = ns("guide_options"),
                        shiny::textInput(ns("label"), label = "Unit label", placeholder = "Enter unit..."),
-                       shiny::checkboxInput(ns("row.label"), label = "Row label", value = row.label),
+                       shiny::checkboxInput(ns("row_label"), label = "Row label", value = row.label),
                        labelUI(ns("labeller")),
-                       shiny::checkboxInput(ns("column.label"), label = "Column label", value = TRUE)
+                       shiny::checkboxInput(ns("column_label"), label = "Column label", value = TRUE)
             )
           )
         ),
@@ -108,7 +108,7 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
   static <- 11000
   interactive <- 3000
   # clear plot
-  clearPlot <- shiny::reactiveVal(FALSE)
+  clear_plot <- shiny::reactiveVal(FALSE)
   # disable downloadButton on init
   shinyjs::disable("download")
 
@@ -118,11 +118,11 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
     if (shiny::is.reactive(clarion)) {
       if (!methods::is(clarion(), "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-      obj <- clarion()$clone(deep = TRUE)
+      clarion()$clone(deep = TRUE)
     } else {
       if (!methods::is(clarion, "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-      obj <- clarion$clone(deep = TRUE)
+      clarion$clone(deep = TRUE)
     }
   })
 
@@ -154,9 +154,9 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
   })
 
   # modules/ ui #####
-  columns <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
-  transform <- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selectedColumns(), with = FALSE])))
-  colorPicker <- shiny::callModule(colorPicker, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(transform$data())))
+  columns <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), column.type.label = "Column types to choose from")
+  transform <- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selected_columns(), with = FALSE])))
+  color <- shiny::callModule(colorPicker, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(transform$data())))
   custom_label <- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data), label = "Select row label", sep = label.sep, disable = shiny::reactive(!input$row.label))
 
   # automatic unitlabel
@@ -169,27 +169,27 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
   shiny::observeEvent(input$reset, {
     log_message("Heatmap: reset", "INFO", token = session$token)
 
-    shinyjs::reset("cluster.distance")
-    shinyjs::reset("cluster.method")
+    shinyjs::reset("cluster_distance")
+    shinyjs::reset("cluster_method")
     shinyjs::reset("clustering")
     shinyjs::reset("distribution")
     shinyjs::reset("label")
-    shinyjs::reset("row.label")
-    shinyjs::reset("column.label")
-    columns <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
-    transform <<- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selectedColumns(), with = FALSE])))
-    colorPicker <<- shiny::callModule(colorPicker, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(transform$data())))
+    shinyjs::reset("row_label")
+    shinyjs::reset("column_label")
+    columns <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), column.type.label = "Column types to choose from")
+    transform <<- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selected_columns(), with = FALSE])))
+    color <<- shiny::callModule(colorPicker, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(transform$data())))
     custom_label <<- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data), label = "Select row label", sep = label.sep, disable = shiny::reactive(!input$row.label))
-    clearPlot(TRUE)
+    clear_plot(TRUE)
   })
 
-  result.data <- shiny::eventReactive(input$plot, {
+  result_data <- shiny::eventReactive(input$plot, {
     # new progress indicator
     progress <- shiny::Progress$new()
     on.exit(progress$close())
     progress$set(0.2, message = "Compute data")
 
-    processed_data <- data.table::data.table(object()$data[, object()$get_uniqueID(), with = FALSE], transform$data())
+    processed_data <- data.table::data.table(object()$data[, object()$get_id(), with = FALSE], transform$data())
 
     progress$set(1)
     return(processed_data)
@@ -200,7 +200,7 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
 
     # enable downloadButton
     shinyjs::enable("download")
-    clearPlot(FALSE)
+    clear_plot(FALSE)
 
     # new progress indicator
     progress <- shiny::Progress$new()
@@ -208,22 +208,22 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
     progress$set(0.2, message = "Compute plot")
 
     plot <- create_heatmap(
-      data = result.data(),
+      data = result_data(),
       unitlabel = input$label,
-      row.label = input$row.label,
+      row.label = input$row_label,
       row.custom.label = custom_label()$label,
-      column.label = input$column.label,
+      column.label = input$column_label,
       column.custom.label = make.unique(columns$label()),
       clustering = input$clustering,
-      clustdist = input$cluster.distance,
-      clustmethod = input$cluster.method,
-      colors = colorPicker()$palette,
+      clustdist = input$cluster_distance,
+      clustmethod = input$cluster_method,
+      colors = color()$palette,
       width = size()$width,
       height = size()$height,
       ppi = size()$ppi,
       scale = size()$scale,
       plot.method = plot.method,
-      winsorize.colors = colorPicker()$winsorize
+      winsorize.colors = color()$winsorize
     )
 
     progress$set(1)
@@ -239,7 +239,7 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
     })
 
     output$interactive <- plotly::renderPlotly({
-      if (clearPlot()) {
+      if (clear_plot()) {
         return()
       } else {
         log_message("Heatmap: render plot interactive", "INFO", token = session$token)
@@ -265,7 +265,7 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
       width = shiny::reactive(plot()$width * (plot()$ppi / 2.54)),
       height = shiny::reactive(plot()$height * (plot()$ppi / 2.54)),
       {
-        if (clearPlot()) {
+        if (clear_plot()) {
           return()
         } else {
           log_message("Heatmap: render plot static", "INFO", token = session$token)
@@ -300,27 +300,27 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
 
   user_input <- shiny::reactive({
     # format selection
-    selection <- list(type = columns$type(), selectedColumns = columns$selectedColumns())
+    selection <- list(type = columns$type(), selectedColumns = columns$selected_columns())
 
     # format clustering
     clustering <- list(
       clustering = input$clustering,
-      distance = input$cluster.distance,
-      method = input$cluster.method
+      distance = input$cluster_distance,
+      method = input$cluster_method
     )
 
     # format options
     options <- list(
       transformation = list(method = transform$method(), applied = transform$transpose()),
-      color = list(distribution = input$distribution, scheme = colorPicker()$name, reverse = colorPicker()$reverse, winsorize = colorPicker()$winsorize),
+      color = list(distribution = input$distribution, scheme = color()$name, reverse = color()$reverse, winsorize = color()$winsorize),
       unit_label = input$label,
-      row_label = input$row.label,
+      row_label = input$row_label,
       custom_row_label = custom_label()$selected,
-      column_label = input$column.label
+      column_label = input$column_label
     )
 
     # merge all
-    all <- list(selection = selection, clustering = clustering, options = options)
+    list(selection = selection, clustering = clustering, options = options)
   })
 
   # notifications #####
@@ -331,20 +331,20 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
     show_warning <- TRUE
 
     # are columns selected?
-    if (shiny::isTruthy(columns$selectedColumns())) {
-      row.num <- nrow(shiny::isolate(object()$data))
-      col.num <- length(columns$selectedColumns())
+    if (shiny::isTruthy(columns$selected_columns())) {
+      row_num <- nrow(shiny::isolate(object()$data))
+      col_num <- length(columns$selected_columns())
 
       # minimal heatmap possible (greater 1x1)?
-      if (row.num > 1 || col.num > 1) {
+      if (row_num > 1 || col_num > 1) {
         # no clustering for single rows or columns
-        if (row.num == 1 && !is.element(input$clustering, c("both", "row"))) {
+        if (row_num == 1 && !is.element(input$clustering, c("both", "row"))) {
           show_warning <- FALSE
           shinyjs::enable("plot")
-        } else if (col.num == 1 && !is.element(input$clustering, c("both", "column"))) {
+        } else if (col_num == 1 && !is.element(input$clustering, c("both", "column"))) {
           show_warning <- FALSE
           shinyjs::enable("plot")
-        } else if (row.num > 1 && col.num > 1) { # no border case heatmaps
+        } else if (row_num > 1 && col_num > 1) { # no border case heatmaps
           show_warning <- FALSE
           shinyjs::enable("plot")
         }
@@ -361,7 +361,7 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
       }
 
       # maximum heatmap reached?
-      if (plot.method == "static" && row.num > static || plot.method == "interactive" && row.num > interactive) {
+      if (plot.method == "static" && row_num > static || plot.method == "interactive" && row_num > interactive) {
         shinyjs::disable("plot")
       }
     }
@@ -424,7 +424,7 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
     rintrojs::introjs(session, options = list(steps = guide()))
   })
 
-  return(result.data)
+  return(result_data)
 }
 
 #' heatmap module guide

From 9e5be22a4d56d3ef86327c09f52073f2bee5cb96 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 11:21:13 +0200
Subject: [PATCH 57/75] lint heatmap

---
 R/heatmap.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/heatmap.R b/R/heatmap.R
index a5d3646..1f25ac4 100644
--- a/R/heatmap.R
+++ b/R/heatmap.R
@@ -157,7 +157,7 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
   columns <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), column.type.label = "Column types to choose from")
   transform <- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selected_columns(), with = FALSE])))
   color <- shiny::callModule(colorPicker, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(transform$data())))
-  custom_label <- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data), label = "Select row label", sep = label.sep, disable = shiny::reactive(!input$row.label))
+  custom_label <- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data), label = "Select row label", sep = label.sep, disable = shiny::reactive(!input$row_label))
 
   # automatic unitlabel
   shiny::observe({
@@ -179,7 +179,7 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
     columns <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), column.type.label = "Column types to choose from")
     transform <<- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(object()$data[, columns$selected_columns(), with = FALSE])))
     color <<- shiny::callModule(colorPicker, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(transform$data())))
-    custom_label <<- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data), label = "Select row label", sep = label.sep, disable = shiny::reactive(!input$row.label))
+    custom_label <<- shiny::callModule(label, "labeller", data = shiny::reactive(object()$data), label = "Select row label", sep = label.sep, disable = shiny::reactive(!input$row_label))
     clear_plot(TRUE)
   })
 
@@ -371,7 +371,7 @@ heatmap <- function(input, output, session, clarion, plot.method = "static", lab
   shiny::observe({
     shiny::req(object())
 
-    if (shiny::isTruthy(columns$selectedColumns())) {
+    if (shiny::isTruthy(columns$selected_columns())) {
       if (input$clustering != "none") { # clustering
         if (plot.method == "static" && nrow(object()$data) > static) { # cluster limitation (static)
           shiny::showNotification(

From 9472f23c4bdc458b011962822cb0f2fcce86ddf1 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 11:24:15 +0200
Subject: [PATCH 58/75] lint label

---
 R/label.R | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/label.R b/R/label.R
index ea3e0b1..6709dab 100644
--- a/R/label.R
+++ b/R/label.R
@@ -31,8 +31,8 @@ labelUI <- function(id){
 #' @export
 label <- function(input, output, session, data, label = "Select label columns", multiple = TRUE, sep = ", ", unique = TRUE, unique_sep = "_", disable = NULL){
   # handle reactive data
-  data.r <- shiny::reactive({
-    if(shiny::is.reactive(data)) {
+  data_r <- shiny::reactive({
+    if (shiny::is.reactive(data)) {
       data()
     } else {
       data
@@ -41,13 +41,13 @@ label <- function(input, output, session, data, label = "Select label columns",
 
   output$label_container <- shiny::renderUI({
     # first choice = "" so no selection for multiple = F is possible
-    shiny::selectizeInput(inputId = session$ns("label_creator"), label = label, choices = c("", names(data.r())), selected = "", multiple = multiple, options = list(placeholder = "None"))
+    shiny::selectizeInput(inputId = session$ns("label_creator"), label = label, choices = c("", names(data_r())), selected = "", multiple = multiple, options = list(placeholder = "None"))
   })
 
   # disable/ enable module
-  if(!is.null(disable)) {
+  if (!is.null(disable)) {
     shiny::observe({
-      if(disable()) {
+      if (disable()) {
         shinyjs::disable("label_creator")
       } else {
         shinyjs::enable("label_creator")
@@ -56,13 +56,13 @@ label <- function(input, output, session, data, label = "Select label columns",
   }
 
   shiny::reactive({
-    if(!shiny::isTruthy(input$label_creator) || !is.null(disable) && disable()) return(NULL)
+    if (!shiny::isTruthy(input$label_creator) || !is.null(disable) && disable()) return(NULL)
 
     # merge selected rows to vector of strings
-    custom_label <- data.r()[, do.call(paste, c(... = .SD, sep = sep)), .SDcols = input$label_creator]
+    custom_label <- data_r()[, do.call(paste, c(... = .SD, sep = sep)), .SDcols = input$label_creator]
 
     # make unique labels
-    if(unique) {
+    if (unique) {
       custom_label <- make.unique(custom_label, sep = unique_sep)
     }
 

From 23900e9e9f893e073dab8c2fc767b0be458c0713 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 11:33:06 +0200
Subject: [PATCH 59/75] lint limit

---
 R/limit.R | 44 ++++++++++++++++++++++----------------------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/R/limit.R b/R/limit.R
index e7499f7..5dac9c6 100644
--- a/R/limit.R
+++ b/R/limit.R
@@ -11,8 +11,8 @@ limitUI <- function(id, label = "Limit"){
 
   shiny::tagList(
     list(shinyjs::useShinyjs(), shiny::checkboxInput(inputId = ns("enable"), label = label, value = FALSE)),
-    shiny::fluidRow(shiny::column(shiny::numericInput(ns("lowerLimit"), label = "Lower limit", value = -2), width = 6),
-                    shiny::column(shiny::numericInput(ns("upperLimit"), label = "Upper limit", value = 2), width = 6))
+    shiny::fluidRow(shiny::column(shiny::numericInput(ns("lower_limit"), label = "Lower limit", value = -2), width = 6),
+                    shiny::column(shiny::numericInput(ns("upper_limit"), label = "Upper limit", value = 2), width = 6))
   )
 }
 
@@ -30,20 +30,20 @@ limitUI <- function(id, label = "Limit"){
 limit <- function(input, output, session, lower = NULL, upper = NULL){
   # reset on re-run
   shinyjs::reset("enable")
-  shinyjs::reset("lowerLimit")
-  shinyjs::reset("upperLimit")
+  shinyjs::reset("lower_limit")
+  shinyjs::reset("upper_limit")
 
   # evaluate reactive parameter
-  lower.r <- shiny::reactive({
-    if(shiny::is.reactive(lower)) {
+  lower_r <- shiny::reactive({
+    if (shiny::is.reactive(lower)) {
       lower()
     } else {
       lower
     }
   })
 
-  upper.r <- shiny::reactive({
-    if(shiny::is.reactive(upper)) {
+  upper_r <- shiny::reactive({
+    if (shiny::is.reactive(upper)) {
       upper()
     } else {
       upper
@@ -52,42 +52,42 @@ limit <- function(input, output, session, lower = NULL, upper = NULL){
 
   # update ui
   shiny::observe({
-    if(!is.null(input$enable) && input$enable) {
-      shiny::isolate(shiny::updateNumericInput(session = session, inputId = "lowerLimit", value = lower.r()))
+    if (!is.null(input$enable) && input$enable) {
+      shiny::isolate(shiny::updateNumericInput(session = session, inputId = "lower_limit", value = lower_r()))
     }
   })
 
   shiny::observe({
-    if(!is.null(input$enable) && input$enable) {
-      shiny::isolate(shiny::updateNumericInput(session = session, inputId = "upperLimit", value = upper.r()))
+    if (!is.null(input$enable) && input$enable) {
+      shiny::isolate(shiny::updateNumericInput(session = session, inputId = "upper_limit", value = upper_r()))
     }
   })
 
   shiny::observe({
     # lowerLimit = smaller than upper
-    shiny::updateNumericInput(session = session, inputId = "lowerLimit", max = input$upperLimit - 1)
+    shiny::updateNumericInput(session = session, inputId = "lower_limit", max = input$upper_limit - 1)
     # upperLimit = greater than lower
-    shiny::updateNumericInput(session = session, inputId = "upperLimit", min = input$lowerLimit + 1)
+    shiny::updateNumericInput(session = session, inputId = "upper_limit", min = input$lower_limit + 1)
   })
 
   # enable ui if checkbox checked
   shiny::observeEvent(input$enable, {
-    if(input$enable) {
-      shinyjs::enable("lowerLimit")
-      shinyjs::enable("upperLimit")
+    if (input$enable) {
+      shinyjs::enable("lower_limit")
+      shinyjs::enable("upper_limit")
     } else {
-      shinyjs::disable("lowerLimit")
-      shinyjs::disable("upperLimit")
+      shinyjs::disable("lower_limit")
+      shinyjs::disable("upper_limit")
     }
   })
 
   # return values
   shiny::reactive({
-    if(!is.null(input$enable) && !input$enable) {
+    if (!is.null(input$enable) && !input$enable) {
       NULL
     } else {
-     list(lower = input$lowerLimit,
-         upper = input$upperLimit)
+     list(lower = input$lower_limit,
+         upper = input$upper_limit)
     }
   })
 }

From 709e387397b5026323f96c9a901ec8d3f1624c99 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 11:36:20 +0200
Subject: [PATCH 60/75] lint marker + example

---
 R/marker.R            | 6 +++---
 exec/marker_example.R | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/marker.R b/R/marker.R
index 511f7f2..7199a99 100644
--- a/R/marker.R
+++ b/R/marker.R
@@ -34,11 +34,11 @@ marker <- function(input, output, session, clarion){
     if (shiny::is.reactive(clarion)) {
       if (!methods::is(clarion(), "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-      obj <- clarion()
+      clarion()
     } else {
       if (!methods::is(clarion, "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-      obj <- clarion
+      clarion
     }
   })
 
@@ -50,7 +50,7 @@ marker <- function(input, output, session, clarion){
     list(
       highlight = shiny::reactive(input$highlight),
       color = shiny::reactive(color()$palette),
-      labelColumn = shiny::reactive(labeller()$selected),
+      label_column = shiny::reactive(labeller()$selected),
       label = shiny::reactive(labeller()$label),
       clarion = object
     )
diff --git a/exec/marker_example.R b/exec/marker_example.R
index e990de3..1dc2939 100644
--- a/exec/marker_example.R
+++ b/exec/marker_example.R
@@ -6,7 +6,7 @@ source("../R/label.R")
 source("../R/limit.R")
 source("../R/clarion.R")
 
-####Test Data
+#### Test Data
 data <- data.table::as.data.table(mtcars, keep.rowname = "id")
 # create metadata
 metadata <- data.table::data.table(names(data), level = c("feature", rep("sample", 7), rep("condition", 4)))
@@ -26,7 +26,7 @@ server <- function(input, output) {
     list(
       highlight = marker$highlight(),
       color = marker$color(),
-      labelColumn = marker$labelColumn(),
+      label_column = marker$label_column(),
       label = marker$label(),
       clarion = marker$clarion()
     )

From 4ac08ad7354ad433cb1e6b26d984b89606e33882 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 12:23:49 +0200
Subject: [PATCH 61/75] lint orNumeric + example

---
 R/orNumeric.R            | 132 +++++++++++++++++++--------------------
 exec/orNumeric_example.R |  18 +++---
 2 files changed, 75 insertions(+), 75 deletions(-)

diff --git a/R/orNumeric.R b/R/orNumeric.R
index a2df084..e430787 100644
--- a/R/orNumeric.R
+++ b/R/orNumeric.R
@@ -43,33 +43,33 @@ orNumericUI <- function(id){
 #' @return Returns a reactive containing a named list with the label, the selected choices as a character vector (text), a boolean vector of length \code{length(choices)} (bool), and a vector of the selected value(s) (value), indicating whether a item has been chosen. If no item has been chosen, the return is \code{TRUE} for items.
 #'
 #' @export
-orNumeric <- function(input, output, session, choices, value, label = "Column", step = 100, stepsize = NULL, min. = shiny::reactive(min(choices.r(), na.rm = TRUE)), max. = shiny::reactive(max(choices.r(), na.rm = TRUE)), label.slider = NULL, zoomable = TRUE, reset = NULL){
-  choices.r <- shiny::reactive({
-    if(shiny::is.reactive(choices)) {
+orNumeric <- function(input, output, session, choices, value, label = "Column", step = 100, stepsize = NULL, min. = shiny::reactive(min(choices_r(), na.rm = TRUE)), max. = shiny::reactive(max(choices_r(), na.rm = TRUE)), label.slider = NULL, zoomable = TRUE, reset = NULL){
+  choices_r <- shiny::reactive({
+    if (shiny::is.reactive(choices)) {
       choices()
     } else {
       choices
     }
   })
 
-  value.r <- shiny::reactive({
-    if(shiny::is.reactive(value)) {
+  value_r <- shiny::reactive({
+    if (shiny::is.reactive(value)) {
       value()
     } else {
       value
     }
   })
 
-  min.r <- shiny::reactive({
-    if(shiny::is.reactive(min.)) {
+  min_r <- shiny::reactive({
+    if (shiny::is.reactive(min.)) {
       min.()
     } else {
       min.
     }
   })
 
-  max.r <- shiny::reactive({
-    if(shiny::is.reactive(max.)) {
+  max_r <- shiny::reactive({
+    if (shiny::is.reactive(max.)) {
       max.()
     } else {
       max.
@@ -81,10 +81,10 @@ orNumeric <- function(input, output, session, choices, value, label = "Column",
   })
 
   output$options <- shiny::renderUI({
-    if(shiny::isolate(length(value.r()) > 1)){
+    if (shiny::isolate(length(value_r()) > 1)) {
       shiny::radioButtons(inputId = session$ns("options"), label = NULL, inline = FALSE,
                                            choices = list("inner", "outer"))
-    }else{
+    } else {
       shiny::selectInput(inputId = session$ns("options"), label = NULL,
                                     choices = c("=", "<", ">"),
                                     selected = NULL,
@@ -95,98 +95,98 @@ orNumeric <- function(input, output, session, choices, value, label = "Column",
   # change css classes so slider visually matches options
   shiny::observe({
       # change css classes if slider is re-rendered
-      min.r()
-      max.r()
+      min_r()
+      max_r()
 
-      if(length(value.r()) > 1){
+      if (length(value_r()) > 1) {
         shiny::req(input$options)
 
-        if(input$options == "inner") {
-          shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"),"')).find('span').removeClass('outer')"))
-          shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"),"')).find('span').addClass('inner')"))
-        } else if(input$options == "outer") {
-          shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"),"')).find('span').removeClass('inner')"))
-          shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"),"')).find('span').addClass('outer')"))
+        if (input$options == "inner") {
+          shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"), "')).find('span').removeClass('outer')"))
+          shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"), "')).find('span').addClass('inner')"))
+        } else if (input$options == "outer") {
+          shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"), "')).find('span').removeClass('inner')"))
+          shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"), "')).find('span').addClass('outer')"))
         }
       } else {
-        shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"),"')).find('span').addClass('empty')"))
+        shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"), "')).find('span').addClass('empty')"))
 
-        if(shiny::isTruthy(input$options)) {
-          if(any(input$options == ">")) {
-            shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"),"')).find('span').addClass('greater')"))
+        if (shiny::isTruthy(input$options)) {
+          if (any(input$options == ">")) {
+            shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"), "')).find('span').addClass('greater')"))
           } else {
-            shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"),"')).find('span').removeClass('greater')"))
+            shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"), "')).find('span').removeClass('greater')"))
           }
 
-          if(any(input$options == "=")) {
-            shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"),"')).find('span').addClass('equal')"))
+          if (any(input$options == "=")) {
+            shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"), "')).find('span').addClass('equal')"))
           } else {
-            shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"),"')).find('span').removeClass('equal')"))
+            shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"), "')).find('span').removeClass('equal')"))
           }
 
-          if(any(input$options == "<")) {
-            shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"),"')).find('span').addClass('less')"))
+          if (any(input$options == "<")) {
+            shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"), "')).find('span').addClass('less')"))
           } else {
-            shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"),"')).find('span').removeClass('less')"))
+            shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"), "')).find('span').removeClass('less')"))
           }
         } else {
-          shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"),"')).find('span').removeClass('greater')"))
-          shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"),"')).find('span').removeClass('equal')"))
-          shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"),"')).find('span').removeClass('less')"))
+          shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"), "')).find('span').removeClass('greater')"))
+          shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"), "')).find('span').removeClass('equal')"))
+          shinyjs::runjs(paste0("$(document.getElementById('", session$ns("slider"), "')).find('span').removeClass('less')"))
         }
       }
   })
 
   output$slider <- shiny::renderUI({
-    min. <- min.r()
-    max. <- max.r()
-    value <- value.r()
+    min. <- min_r()
+    max. <- max_r()
+    value <- value_r()
 
     interval <- ifelse(is.null(stepsize), abs(min. - max.) / step, stepsize)
 
     out <- shiny::tagList(
       shiny::fluidRow(
-        if(zoomable) shiny::column(width = 3, shiny::numericInput(session$ns("minVal"), min = min., max = max., value = min., label = NULL, width = "100%")),
+        if (zoomable) shiny::column(width = 3, shiny::numericInput(session$ns("min_val"), min = min., max = max., value = min., label = NULL, width = "100%")),
         shiny::column(width = ifelse(zoomable, 6, 12), shiny::sliderInput(session$ns("slider"), label = label.slider, min = min., max = max., value = value, step = interval, width  = "100%", round = FALSE)),
-        if(zoomable) shiny::column(width = 3, shiny::numericInput(session$ns("maxVal"), min = min., max = max., value = max., label = NULL, width = "100%"))
+        if (zoomable) shiny::column(width = 3, shiny::numericInput(session$ns("max_val"), min = min., max = max., value = max., label = NULL, width = "100%"))
       )
     )
 
     return(out)
   })
 
-  if(shiny::is.reactive(reset)) {
+  if (shiny::is.reactive(reset)) {
     shiny::observeEvent(reset(), {
       # require rendered UI
       shiny::req(input$slider)
 
-      shinyjs::reset("minVal")
-      shinyjs::reset("maxVal")
+      shinyjs::reset("min_val")
+      shinyjs::reset("max_val")
       shinyjs::reset("options")
 
-      min. <- min.r()
-      max. <- max.r()
-      value <- value.r()
+      min. <- min_r()
+      max. <- max_r()
+      value <- value_r()
       interval <- ifelse(is.null(stepsize), abs(min. - max.) / step, stepsize)
       shiny::updateSliderInput(session = session, inputId = "slider", value = value, min = min., max = max., step = interval) # shinyjs::reset("slider") won't reset value if not in current range
     })
   }
 
-  if(zoomable){
-    #zoomable slider
+  if (zoomable) {
+    # zoomable slider
     shiny::observe({
-      shiny::req(input$minVal, input$maxVal)
+      shiny::req(input$min_val, input$max_val)
 
-      interval <- ifelse(is.null(stepsize), abs(input$minVal - input$maxVal) / step, stepsize)
-      shiny::updateSliderInput(session, inputId = "slider", min = input$minVal, max = input$maxVal, step = interval)
+      interval <- ifelse(is.null(stepsize), abs(input$min_val - input$max_val) / step, stepsize)
+      shiny::updateSliderInput(session, inputId = "slider", min = input$min_val, max = input$max_val, step = interval)
     })
 
-    #only useful values
+    # only useful values
     shiny::observe({
-      shiny::req(input$minVal, input$maxVal)
+      shiny::req(input$min_val, input$max_val)
 
-      shiny::updateNumericInput(session, inputId = "minVal", max  = input$maxVal)
-      shiny::updateNumericInput(session, inputId = "maxVal", min = input$minVal)
+      shiny::updateNumericInput(session, inputId = "min_val", max  = input$max_val)
+      shiny::updateNumericInput(session, inputId = "max_val", min = input$min_val)
     })
   }
 
@@ -194,27 +194,27 @@ orNumeric <- function(input, output, session, choices, value, label = "Column",
   output$info <- shiny::renderUI({
     shiny::tagList(
       #added css so that padding won't be added everytime (sums up) modal is shown
-      shiny::tags$style(type="text/css", "body {padding-right: 0px !important;}"),
+      shiny::tags$style(type = "text/css", "body {padding-right: 0px !important;}"),
       shiny::actionLink(session$ns("infobutton"), label = NULL, icon = shiny::icon("question-circle"))
     )
   })
 
   #show right info
   shiny::observeEvent(input$infobutton, {
-    if(length(value.r()) > 1){
-      #ranged slider
+    if (length(value_r()) > 1) {
+      # ranged slider
       title <- "Numeric"
       content <- shiny::HTML("Use the slider to selected the desired range. Choose either 'inner' or 'outer' for the values in- or outside the range.")
     }else{
-      #single slider
+      # single slider
       title <- "Numeric"
       content <- shiny::HTML("Select one or more operations (\"<\", \">\", \"=\")<br/> Use slider to set value on which operations will be performed.<br/> E.g. If you choose \"<\" \"=\" 5 every value smaller or equal will be selected.")
     }
 
-    if(zoomable){
+    if (zoomable) {
       content <- shiny::HTML(content, paste("<hr> Use the numberfields on each side of the slider to set it's min/max value, allowing for a more precise selection. As the slider will always attempt to have", step, "steps."))
       path <- "wilson_www/orNumeric_help.png"
-      if(length(value.r()) > 1) content <- shiny::tagList(content, shiny::div(shiny::img(src = path, width = "90%")))
+      if (length(value_r()) > 1) content <- shiny::tagList(content, shiny::div(shiny::img(src = path, width = "90%")))
     }
 
     shiny::showModal(
@@ -229,23 +229,23 @@ orNumeric <- function(input, output, session, choices, value, label = "Column",
   })
 
   selected <- shiny::reactive({
-    searchData(input = input$slider, choices = choices.r(), options = input$options, min. = min.r(), max. = max.r())
+    searchData(input = input$slider, choices = choices_r(), options = input$options, min. = min_r(), max. = max_r())
   })
 
   out <- shiny::reactive({
-    value <- value.r()
+    value <- value_r()
 
     text <- ""
 
     # ranged: return text if not in default selection; single: return if options are selected
-    if(length(value) > 1) {
-      if(shiny::isTruthy(input$slider) & shiny::isTruthy(input$options)) {
-        if(!(input$slider[1] == min.r() & input$slider[2] == max.r() & input$options == "inner")) {
+    if (length(value) > 1) {
+      if (shiny::isTruthy(input$slider) & shiny::isTruthy(input$options)) {
+        if (!(input$slider[1] == min_r() & input$slider[2] == max_r() & input$options == "inner")) {
           text <- paste(input$options, paste(input$slider, collapse = "-"))
         }
       }
     } else {
-      if(shiny::isTruthy(input$options)){
+      if (shiny::isTruthy(input$options)) {
         text <- paste(paste(input$options, collapse = " "), input$slider)
       }
     }
diff --git a/exec/orNumeric_example.R b/exec/orNumeric_example.R
index 0e9fc24..9be5dca 100644
--- a/exec/orNumeric_example.R
+++ b/exec/orNumeric_example.R
@@ -10,20 +10,20 @@ ui <- fluidPage(
   tags$br(),
   column(width = 6,
          orNumericUI(id = "ranged"),
-         verbatimTextOutput("ran.out")
+         verbatimTextOutput("ran_out")
          ),
   column(width = 6,
          orNumericUI(id = "single"),
-         verbatimTextOutput("sin.out")
+         verbatimTextOutput("sin_out")
          )
 )
 
 server <- function(input, output) {
-  choices1 <- c(0,1,2,3,4,5,6,7,8,9,10)
-  choices2 <- c(11, 12, 13, 14, 15, 16, 17, 18, 19, 20)
+  choices1 <- c(0:10)
+  choices2 <- c(11:20)
 
   choices <- reactive({
-    if(input$test == 1) {
+    if (input$test == 1) {
       choices1
     } else {
       choices2
@@ -36,11 +36,11 @@ server <- function(input, output) {
     c(min(choices()), max(choices()))
   })
 
-  single <-callModule(orNumeric, "single", choices = choices, value = 3, label = "Title single", step = 11, zoomable = FALSE, reset = reactive(input$reset))
-  ranged <-callModule(orNumeric, "ranged", choices = choices, value = value, label = "Title ranged", stepsize = 1, reset = reactive(input$reset))
+  single <- callModule(orNumeric, "single", choices = choices, value = 3, label = "Title single", step = 11, zoomable = FALSE, reset = reactive(input$reset))
+  ranged <- callModule(orNumeric, "ranged", choices = choices, value = value, label = "Title ranged", stepsize = 1, reset = reactive(input$reset))
 
-  output$ran.out <- renderPrint(ranged())
-  output$sin.out <- renderPrint(single())
+  output$ran_out <- renderPrint(ranged())
+  output$sin_out <- renderPrint(single())
 }
 
 # Run the application

From 7c6547f484d54331b1990bc8fb44dba6e0184176 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 12:32:29 +0200
Subject: [PATCH 62/75] lint orTextual + example

---
 R/orTextual.R            | 54 ++++++++++++++++++++--------------------
 exec/orTextual_example.R | 14 +++++------
 2 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/R/orTextual.R b/R/orTextual.R
index a51e073..c070544 100644
--- a/R/orTextual.R
+++ b/R/orTextual.R
@@ -37,10 +37,10 @@ orTextualUI <- function(id){
 #'
 #' @export
 orTextual <- function(input, output, session, choices, selected = NULL, label = "Column", delimiter = NULL, multiple = TRUE, contains = FALSE, reset = NULL){
-  raw.choices <- choices
+  raw_choices <- choices
 
-  #delimit choices
-  if(!is.null(delimiter) & contains == FALSE){
+  # delimit choices
+  if (!is.null(delimiter) & contains == FALSE) {
     choices <- unlist(strsplit(choices, split = delimiter, fixed = TRUE))
   }
 
@@ -49,11 +49,11 @@ orTextual <- function(input, output, session, choices, selected = NULL, label =
   })
 
   output$select <- shiny::renderUI({
-    if(contains){
+    if (contains) {
       ui <- shiny::textInput(session$ns("column"), label = NULL)
-    }else{
+    } else {
       ui <- shiny::selectizeInput(session$ns("column"), label = NULL, choices = NULL, multiple = multiple, selected = NULL)
-      #only fetch needed data (calculation on server-side)
+      # only fetch needed data (calculation on server-side)
       shiny::updateSelectizeInput(session, "column", choices = unique(choices), selected = selected, server = TRUE)
     }
 
@@ -62,28 +62,28 @@ orTextual <- function(input, output, session, choices, selected = NULL, label =
 
   output$info <- shiny::renderUI({
     shiny::tagList(
-      #added css so that padding won't be added everytime (sums up) modal is shown
-      shiny::tags$style(type="text/css", "body {padding-right: 0px !important;}"),
+      # added css so that padding won't be added everytime (sums up) modal is shown
+      shiny::tags$style(type = "text/css", "body {padding-right: 0px !important;}"),
       shiny::actionLink(session$ns("infobutton"), label = NULL, icon = shiny::icon("question-circle"))
     )
   })
 
-  if(shiny::is.reactive(reset)) {
+  if (shiny::is.reactive(reset)) {
     shiny::observeEvent(reset(), {
-      if(is.null(selected)){
+      if (is.null(selected)) {
         shinyjs::reset("column")
-      }else{
+      } else {
         shiny::updateSelectizeInput(session, "column", selected = selected)
       }
     })
   }
 
-  #show right info
+  # show right info
   shiny::observeEvent(input$infobutton, {
-    if(contains){
+    if (contains) {
       title <- "Textsearch"
       content <- shiny::HTML("Enter some text which will be used for textsearch.")
-    }else{
+    } else {
       title <- "Text"
       content <- shiny::HTML("Select one or multiple values to filter.")
     }
@@ -98,27 +98,27 @@ orTextual <- function(input, output, session, choices, selected = NULL, label =
     )
   })
 
-  selected.choices <- shiny::reactive({
-    if(!is.null(input$column)){
-      #escape all regex symbols
-      esc.choices <- paste0("\\Q", input$column, "\\E")
+  selected_choices <- shiny::reactive({
+    if (!is.null(input$column)) {
+      # escape all regex symbols
+      esc_choices <- paste0("\\Q", input$column, "\\E")
 
-      if(contains | !is.null(delimiter)){
-        result <- grepl(pattern = paste0(esc.choices, paste0("($|", delimiter, ")"), collapse = "|"), raw.choices, perl = TRUE)
-      }else{
-        result <- grepl(pattern = paste0("^(", esc.choices, ")$", collapse = "|"), raw.choices, perl = TRUE)
+      if (contains | !is.null(delimiter)) {
+        result <- grepl(pattern = paste0(esc_choices, paste0("($|", delimiter, ")"), collapse = "|"), raw_choices, perl = TRUE)
+      } else {
+        result <- grepl(pattern = paste0("^(", esc_choices, ")$", collapse = "|"), raw_choices, perl = TRUE)
       }
 
-      #set all TRUE if nothing selected
-      if(is.null(input$column) | input$column[1] == "" & !all(result)){
+      # set all TRUE if nothing selected
+      if (is.null(input$column) | input$column[1] == "" & !all(result)) {
         result <- !result
       }
 
       return(result)
-    }else{
-      return(!logical(length = length(raw.choices)))
+    } else {
+      return(!logical(length = length(raw_choices)))
     }
   })
 
-  return(shiny::reactive(list(label = label, bool = selected.choices(), text = input$column)))
+  return(shiny::reactive(list(label = label, bool = selected_choices(), text = input$column)))
 }
diff --git a/exec/orTextual_example.R b/exec/orTextual_example.R
index 374a163..02ddc26 100644
--- a/exec/orTextual_example.R
+++ b/exec/orTextual_example.R
@@ -6,15 +6,15 @@ ui <- fluidPage(
   h4('choices <- c("test,1,a,v,asd", "a,b,c", "a,b,c", "asd|lkj", "2")'),
   column(width = 4,
            orTextualUI(id = "contains"),
-         verbatimTextOutput("co.out")
+         verbatimTextOutput("co_out")
            ),
   column(width = 4,
           orTextualUI(id = "delimit"),
-         verbatimTextOutput("del.out")
+         verbatimTextOutput("del_out")
          ),
   column(width = 4,
          orTextualUI(id = "nodelimit"),
-         verbatimTextOutput("nodel.out")
+         verbatimTextOutput("nodel_out")
          ),
   actionButton("button", "reset")
 )
@@ -24,11 +24,11 @@ server <- function(input, output) {
 
   contains <- callModule(orTextual, "contains", choices = choices, label = "contains = TRUE", contains = TRUE, reset = reactive(input$button))
   delimit <- callModule(orTextual, "delimit", choices = choices, label = "delimiter = ','", delimiter = ",", reset = reactive(input$button))
-  no.delimit <- callModule(orTextual, "nodelimit", choices = choices, label = "delimiter = NULL, selected = 2, multiple = FALSE", selected = "2", multiple = FALSE, reset = reactive(input$button))
+  no_delimit <- callModule(orTextual, "nodelimit", choices = choices, label = "delimiter = NULL, selected = 2, multiple = FALSE", selected = "2", multiple = FALSE, reset = reactive(input$button))
 
-  output$co.out <- renderPrint(contains())
-  output$del.out <- renderPrint(delimit())
-  output$nodel.out <- renderPrint(no.delimit())
+  output$co_out <- renderPrint(contains())
+  output$del_out <- renderPrint(delimit())
+  output$nodel_out <- renderPrint(no_delimit())
 }
 
 # Run the application

From 527e928953d2d1cc9f00dd41bfe6d62b5b4a23c1 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 12:52:11 +0200
Subject: [PATCH 63/75] lint orNumeric

---
 man/orNumeric.Rd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/man/orNumeric.Rd b/man/orNumeric.Rd
index 329c270..ee9a85e 100644
--- a/man/orNumeric.Rd
+++ b/man/orNumeric.Rd
@@ -5,8 +5,8 @@
 \title{orNumeric module server logic}
 \usage{
 orNumeric(input, output, session, choices, value, label = "Column",
-  step = 100, stepsize = NULL, min. = shiny::reactive(min(choices.r(),
-  na.rm = TRUE)), max. = shiny::reactive(max(choices.r(), na.rm = TRUE)),
+  step = 100, stepsize = NULL, min. = shiny::reactive(min(choices_r(),
+  na.rm = TRUE)), max. = shiny::reactive(max(choices_r(), na.rm = TRUE)),
   label.slider = NULL, zoomable = TRUE, reset = NULL)
 }
 \arguments{

From a5468a120c5ce9ab8c8c803691dbd55243edf82f Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 12:52:28 +0200
Subject: [PATCH 64/75] lint parser

---
 R/parser.R | 179 ++++++++++++++++++++++++++---------------------------
 1 file changed, 89 insertions(+), 90 deletions(-)

diff --git a/R/parser.R b/R/parser.R
index 7df2e6c..9827548 100644
--- a/R/parser.R
+++ b/R/parser.R
@@ -27,24 +27,24 @@
 #'
 #' @export
 parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduced, config = system.file("extdata", "parser_MaxQuant_config.json", package = "wilson"), delimiter = ";", format = NULL, version = NULL, experiment_id = NULL){
-  if(missing(proteinGroups_in)){
+  if (missing(proteinGroups_in)) {
     stop("The proteinGroups file was not given")
   }
-  if(missing(summary_in)){
+  if (missing(summary_in)) {
     stop("The summary file was not given")
   }
-  if(missing(outfile)){
+  if (missing(outfile)) {
     stop("The output file was not given")
   }
-  if(missing(outfile_reduced)){
+  if (missing(outfile_reduced)) {
     stop("The output_reduced file was not given")
   }
 
   # parsers json config file
   # @param config path of config file
   # @return data.table with metadata
-  get_meta_from_config <- function(meta_config){
-    dr <- lapply(meta_config$meta, function(r){
+  get_meta_from_config <- function(meta_config) {
+    dr <- lapply(meta_config$meta, function(r) {
       data.table::data.table("col_name" = r$col_name,
                                  "level" = r$level,
                                  "type" = r$type,
@@ -52,7 +52,7 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
                                  "sublabel" = r$sublabel
                                 )
     })
-    meta <- do.call('rbind', dr)
+    do.call("rbind", dr)
   }
 
 
@@ -63,38 +63,37 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
 
   # @param scores,ratios,category,ary vectors with Strings
   # @return String type of given column
-  get_sample_type <- function(name, scores, ratios, prob, category, ary){
+  get_sample_type <- function(name, scores, ratios, prob, category, ary) {
 
     name_split <- strsplit(name, " ")
-    if(grepl("[[:digit:]]{1,2}",utils::tail(name_split[[1]],1))){
-      name <- paste(utils::head(name_split[[1]], -1), collapse = ' ')
+    if (grepl("[[:digit:]]{1,2}", utils::tail(name_split[[1]], 1))) {
+      name <- paste(utils::head(name_split[[1]], -1), collapse = " ")
     }
-    if(name %in% scores){ return("score") }
-    if(name %in% ratios){ return("ratio") }
-    if(name %in% prob){ return("probability")}
-    if(name %in% category){ return("category") }
-    if(name %in% ary){ return("array") }
+    if (name %in% scores) return("score")
+    if (name %in% ratios) return("ratio")
+    if (name %in% prob) return("probability")
+    if (name %in% category) return("category")
+    if (name %in% ary) return("array")
 
     return("unknown")
   }
 
-
   # Get the level of the sample column
   # Checking for keywords inside of the column name
   # Each keyword is given one level
   # @param col_head column head
   # @return String level of given column
-  get_sample_level <- function(col_head, isSample, full_list){
+  get_sample_level <- function(col_head, isSample, full_list) {
     # Get the level of all 'sample' columns.
     # Default: level <- "sample"
-    if(grepl("Ratio", col_head, perl = TRUE)){
-      if (grepl("type", col_head, perl = TRUE)){ return("feature") }
+    if (grepl("Ratio", col_head, perl = TRUE)) {
+      if (grepl("type", col_head, perl = TRUE)) return("feature")
       return("contrast")
     }
-    if (grepl("type", col_head, perl = TRUE)){ return("feature") }
-    if(grepl("Fraction [[:digit:]]{1,2}", col_head, perl = TRUE)){ return("condition") }
-    if(isSample){ return("sample") }
-    if(col_head %in% full_list){ return("contrast") }
+    if (grepl("type", col_head, perl = TRUE)) return("feature")
+    if (grepl("Fraction [[:digit:]]{1,2}", col_head, perl = TRUE)) return("condition")
+    if (isSample) return("sample")
+    if (col_head %in% full_list) return("contrast")
     return("unknown")
   }
 
@@ -103,15 +102,15 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
   # remaining columns <- columns which are not in meta or a sample column
   # @param col_head column head
   # @return list with label and sublabel
-  get_remaining_labeling <- function(col_head){
-    col_head_split = strsplit(col_head, " ")
-    if(length(col_head_split) > 1){
+  get_remaining_labeling <- function(col_head) {
+    col_head_split <- strsplit(col_head, " ")
+    if (length(col_head_split) > 1) {
       sublabel <- col_head_split[[1]][length(col_head_split[[1]])]
-      if(grepl(sublabel, "[%]", fixed = TRUE)){
-        label <- paste(utils::head(col_head_split[[1]], -2), collapse = ' ')
-        sublabel <- paste(utils::tail(col_head_split[[1]], 2), collapse = ' ')
+      if (grepl(sublabel, "[%]", fixed = TRUE)) {
+        label <- paste(utils::head(col_head_split[[1]], -2), collapse = " ")
+        sublabel <- paste(utils::tail(col_head_split[[1]], 2), collapse = " ")
       } else {
-        label <- paste(utils::head(col_head_split[[1]], -1), collapse = ' ')
+        label <- paste(utils::head(col_head_split[[1]], -1), collapse = " ")
         sublabel <- col_head_split[[1]][length(col_head_split[[1]])]
       }
       return(list(label, sublabel))
@@ -126,26 +125,26 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
   # @param exp_names list of experiment names
   # @param col_names list of all column names
   # @return list: 1 <- list of all reduced column names, 2 <- columns which are in the raw list but not in the final list
-  get_reduced_version <- function(meta_full, reduced_list, exp_names, col_names){
+  get_reduced_version <- function(meta_full, reduced_list, exp_names, col_names) {
     red_split <- strsplit(reduced_list, ";")
-    red_exp_list <- unlist(lapply(red_split, function(split_name){
+    red_exp_list <- unlist(lapply(red_split, function(split_name) {
       # if length == 2 entry of reduced list is column_name;exp
       # only adding column_name + experiment name to the list
-      if(length(split_name) == 2){
-        red_col_name <- lapply(exp_names, function(exp_name){
-          rcn <- paste(split_name[1],exp_name)
+      if (length(split_name) == 2) {
+        red_col_name <- lapply(exp_names, function(exp_name) {
+          rcn <- paste(split_name[1], exp_name)
           # special case for Sequence Coverage exp_name [%]
-          if(!(rcn %in% col_names) && (paste(rcn,"[%]") %in% col_names)){
-            rcn <- paste(rcn,"[%]")
+          if (!(rcn %in% col_names) && (paste(rcn, "[%]") %in% col_names)) {
+            rcn <- paste(rcn, "[%]")
           }
           return(rcn)
         })
       } else {
         # adding both column name +  experiment_name and column name without experiment name to list
-        red_col_name <- lapply(1:(length(exp_names)+1), function(i){
-          if(i <= length(exp_names)){
-            if(paste(split_name,exp_names[i]) %in% col_names){
-              return(paste(split_name,exp_names[i]))
+        red_col_name <- lapply(1:(length(exp_names) + 1), function(i) {
+          if (i <= length(exp_names)) {
+            if (paste(split_name, exp_names[i]) %in% col_names) {
+              return(paste(split_name, exp_names[i]))
             }
           } else {
             return(split_name)
@@ -155,7 +154,7 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
     }))
     overlap <- setdiff(red_exp_list, col_names)
     red_exp_list <- red_exp_list[!(red_exp_list %in% overlap)]
-    return(list(red_exp_list,overlap))
+    return(list(red_exp_list, overlap))
   }
 
 
@@ -167,32 +166,32 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
   # @param exp_id experiment id
   # @param pGroups data table protein groups file
   write_clarion_file <- function(meta, out, format, version, exp_id, pGroups, delimiter){
-    to_append = FALSE
-    if(!missing(format)){
-      write(paste0("!format=",format),file=out, append = to_append)
-      to_append = TRUE
+    to_append <- FALSE
+    if (!missing(format)) {
+      write(paste0("!format=", format), file = out, append = to_append)
+      to_append <- TRUE
     }
-    if(!missing(version)){
-      write(paste0("!version=",version),file=out, append = to_append)
-      to_append = TRUE
+    if (!missing(version)) {
+      write(paste0("!version=", version), file = out, append = to_append)
+      to_append <- TRUE
     }
-    if(!missing(exp_id)){
-      write(paste0("!experiment_id=",exp_id),file=out, append = to_append)
-      to_append = TRUE
+    if (!missing(exp_id)) {
+      write(paste0("!experiment_id=", exp_id), file = out, append = to_append)
+      to_append <- TRUE
     }
-    write(paste0("!delimiter=",delimiter),file=out, append=to_append)
-    write("#key\tfactor1\tlevel\ttype\tlabel\tsub_label",file=out, append=TRUE)
-    data.table::fwrite(meta, file=out, sep = "\t", append=TRUE, col.names=FALSE, quote= FALSE)
-    data.table::fwrite(pGroups, file=out, sep = "\t", append=TRUE, col.names = TRUE, quote= FALSE)
+    write(paste0("!delimiter=", delimiter), file = out, append = to_append)
+    write("#key\tfactor1\tlevel\ttype\tlabel\tsub_label", file = out, append = TRUE)
+    data.table::fwrite(meta, file = out, sep = "\t", append = TRUE, col.names = FALSE, quote = FALSE)
+    data.table::fwrite(pGroups, file = out, sep = "\t", append = TRUE, col.names = TRUE, quote = FALSE)
   }
 
   # reading files in data tables
-  proteinGroups <- data.table::fread(proteinGroups_in, header = TRUE, quote='')
+  proteinGroups <- data.table::fread(proteinGroups_in, header = TRUE, quote = "")
   summary_file <- data.table::fread(summary_in, header = TRUE)
   meta_config <- rjson::fromJSON(file = config)
 
   # getting experiment names
-  exp_names <- (unique(summary_file[Experiment != "",Experiment]))
+  exp_names <- (unique(summary_file[Experiment != "", Experiment]))
 
   meta <- get_meta_from_config(meta_config = meta_config)
 
@@ -213,36 +212,36 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
 
   # get metadata for each sample column
   # append rows to data table with metadata
-  samples_list <- lapply(col_names, function(col_head){
+  samples_list <- lapply(col_names, function(col_head) {
 
     unlist(lapply(exp_names, function(name){
       name_brackets <- paste0("\\Q", name)
       exp_regex <- paste0("\\Q ", name)
       sample_description <- strsplit(col_head, exp_regex)
-      if(length(grep(name_brackets, col_head, perl = TRUE)) == 1 ){  # Does column name contains experiment name?
-        de<-data.table::data.table("col_name" = c(col_head),
-                                   "level" = c(get_sample_level(col_head = col_head,isSample =  TRUE, full_list = full_sample_list)),
+      if (length(grep(name_brackets, col_head, perl = TRUE)) == 1 ) {  # Does column name contains experiment name?
+        de <- data.table::data.table("col_name" = c(col_head),
+                                   "level" = c(get_sample_level(col_head = col_head, isSample =  TRUE, full_list = full_sample_list)),
                                    "type" = c(get_sample_type(name = sample_description[[1]][1], scores =  sample_scores,
                                                               ratios = sample_ratios, prob = sample_probability, category =  sample_category,
                                                               ary =  sample_ary)),
                                    "label" = c(name),
-                                   "sublabel" = c(trimws(gsub(name_brackets, '', col_head), "r"))
+                                   "sublabel" = c(trimws(gsub(name_brackets, "", col_head), "r"))
         )
         return(de)
       }
     }))
 
   })
-  samples <- do.call('rbind', Filter(Negate(is.null), samples_list))
+  samples <- do.call("rbind", Filter(Negate(is.null), samples_list))
   meta_half <- rbind(meta_trim, samples)
 
   # get metadata for each remaining column(columsn which are specific for a certain quantification methode)
   # append rows to data table with metadata
-  remaining_list <- lapply(col_names, function(col_head){
-    if(!(col_head %in% meta_half[["col_name"]])){
+  remaining_list <- lapply(col_names, function(col_head) {
+    if (!(col_head %in% meta_half[["col_name"]])) {
       label_sublabel <- get_remaining_labeling(col_head = col_head)
-      de2<-data.table::data.table("col_name" = c(col_head),
-                                  "level" =c(get_sample_level(col_head = col_head,isSample =  FALSE, full_list = full_sample_list)),
+      de2 <- data.table::data.table("col_name" = c(col_head),
+                                  "level" = c(get_sample_level(col_head = col_head, isSample =  FALSE, full_list = full_sample_list)),
                                   "type" = c(get_sample_type(name = col_head, scores = sample_scores, ratios =  sample_ratios,
                                                              prob = sample_probability, category = sample_category, ary = sample_ary)),
                                   "label" = c(label_sublabel[1]),
@@ -251,40 +250,40 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
       return(de2)
     }
   })
-  remaining <- do.call('rbind', Filter(Negate(is.null), remaining_list))
+  remaining <- do.call("rbind", Filter(Negate(is.null), remaining_list))
   meta_full <- rbind(meta_half, remaining)
-  meta_full$col_name <- sub("^","#",meta_full$col_name)
+  meta_full$col_name <- sub("^", "#", meta_full$col_name)
 
   # add column factor 1 and reorder the columns
   meta_full$factor1 <- ""
   meta_full <- meta_full[, c("col_name", "factor1", "level", "type", "label", "sublabel")]
 
   # get data.table with reduced metadata
-  reduced <- get_reduced_version(meta_full = meta_full,reduced_list =  reduced_list,
+  reduced <- get_reduced_version(meta_full = meta_full, reduced_list =  reduced_list,
                                  exp_names = exp_names, col_names = col_names)
-  meta_reduced <- meta_full[meta_full$col_name %in% sub("^","#",reduced[[1]]),]
+  meta_reduced <- meta_full[meta_full$col_name %in% sub("^", "#", reduced[[1]]), ]
 
   # if there are unknown columns the user gets a warning with all unknown columns
   # unknown columns wont be writen in the meta data header
-  if(nrow(meta_full[level == "unknown"]) > 0){
-    meta_warn <- gsub("#","",meta_full[level == "unknown",col_name])
-    warning("Following columns are unknown and have been removed (Check JSON config file: 'meta'): ", paste(meta_warn, collapse=", "))
+  if (nrow(meta_full[level == "unknown"]) > 0) {
+    meta_warn <- gsub("#", "", meta_full[level == "unknown", col_name])
+    warning("Following columns are unknown and have been removed (Check JSON config file: 'meta'): ", paste(meta_warn, collapse = ", "))
     meta_full <- meta_full[level != "unknown"]
   }
 
   # if there are unknown column types the user gets a warning with all columns with unknown type
   # columns with unknown types wont be writen in the meta data header
-  if(nrow(meta_full[type == "unknown"]) > 0){
-    meta_warn <- gsub("#","",meta_full[type == "unknown",col_name])
-    warning("Due to unknown type follwing columns were removed (Check JSON config file: 'type_X'): ", paste(meta_warn, collapse=", "))
+  if (nrow(meta_full[type == "unknown"]) > 0) {
+    meta_warn <- gsub("#", "", meta_full[type == "unknown", col_name])
+    warning("Due to unknown type follwing columns were removed (Check JSON config file: 'type_X'): ", paste(meta_warn, collapse = ", "))
     meta_full <- meta_full[type != "unknown"]
   }
 
   # writing advanced CLARION file
   write_clarion_file(meta = meta_full, out = outfile, format =  format,
-                     version =  version, exp_id = experiment_id, pGroups = proteinGroups, delimiter = delimiter)
+                     version = version, exp_id = experiment_id, pGroups = proteinGroups, delimiter = delimiter)
 
-  #writing reduced CLARION file
+  # writing reduced CLARION file
   write_clarion_file(meta = meta_reduced, out = outfile_reduced, format = format,
                      version = version, exp_id = experiment_id, pGroups = proteinGroups, delimiter = delimiter)
 }
@@ -304,17 +303,17 @@ parser <- function(file, dec = ".") {
 
   # number of rows for each part
   con <- file(file, open = "r")
-  num.header <- 0
-  num.metadata <- 0
+  num_header <- 0
+  num_metadata <- 0
 
   tryCatch(expr = {
     while (TRUE) {
       line <- readLines(con = con, n = 1)
 
       if (grepl("^!", line, perl = TRUE)) {
-        num.header <- num.header + 1
+        num_header <- num_header + 1
       } else if (grepl("^#", line, perl = TRUE)) {
-        num.metadata <- num.metadata + 1
+        num_metadata <- num_metadata + 1
       } else {
         break
       }
@@ -324,14 +323,14 @@ parser <- function(file, dec = ".") {
   })
 
   ### parse header
-  if (num.header > 0) {
-    header <- data.table::fread(input = file, fill = TRUE, header = FALSE, dec = dec, nrows = num.header, integer64 = "double")
+  if (num_header > 0) {
+    header <- data.table::fread(input = file, fill = TRUE, header = FALSE, dec = dec, nrows = num_header, integer64 = "double")
     # cut of leading !
     header <- as.list(gsub("^!", "", header[[1]]))
     # make named list
-    header.names <- gsub("=.*$", "", header, perl = TRUE)
+    header_names <- gsub("=.*$", "", header, perl = TRUE)
     header <- as.list(gsub("^.*?=", "", header, perl = TRUE))
-    names(header) <- header.names
+    names(header) <- header_names
     # remove quotes from delimiter
     if (!is.null(header$delimiter) && grepl(header$delimiter, pattern = '^".*"$', perl = TRUE)) {
       header$delimiter <- substr(header$delimiter, start = 2, stop = nchar(header$delimiter) - 1)
@@ -341,7 +340,7 @@ parser <- function(file, dec = ".") {
   }
 
   ### parse metadata
-  metadata <- data.table::fread(input = file, skip = num.header, header = FALSE, nrows = num.metadata, fill = TRUE, dec = dec, integer64 = "double")
+  metadata <- data.table::fread(input = file, skip = num_header, header = FALSE, nrows = num_metadata, fill = TRUE, dec = dec, integer64 = "double")
   # cut off leading #
   metadata[, names(metadata)[1] := gsub("^#", "", metadata[[1]])]
   # set first line as header
@@ -354,7 +353,7 @@ parser <- function(file, dec = ".") {
   metadata <- metadata[-1]
 
   ### parse data
-  data <- data.table::fread(input = file, header = TRUE, skip = num.header + num.metadata, fill = FALSE, dec = dec, integer64 = "double")
+  data <- data.table::fread(input = file, header = TRUE, skip = num_header + num_metadata, fill = FALSE, dec = dec, integer64 = "double")
 
   data.table::setindexv(metadata, names(metadata)[1])
   data.table::setindexv(data, names(data)[1])

From 45d08082a852574b12ba29ef347578d9da5a36ea Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 13:10:44 +0200
Subject: [PATCH 65/75] lint pca

---
 R/pca.R | 74 ++++++++++++++++++++++++++++-----------------------------
 1 file changed, 37 insertions(+), 37 deletions(-)

diff --git a/R/pca.R b/R/pca.R
index 9ac43f4..6dade4a 100644
--- a/R/pca.R
+++ b/R/pca.R
@@ -33,8 +33,8 @@ pcaUI <- function(id, show.label = TRUE) {
           shiny::column(
             width = 4,
             shiny::div(id = ns("guide_dimensions"),
-                       shiny::numericInput(ns("dimA"), label = "PCA dimension (x-axis)", min = 1, max = 6, step = 1, value = 1),
-                       shiny::numericInput(ns("dimB"), label = "PCA dimension (y-axis)", min = 1, max = 6, step = 1, value = 2)
+                       shiny::numericInput(ns("dim_a"), label = "PCA dimension (x-axis)", min = 1, max = 6, step = 1, value = 1),
+                       shiny::numericInput(ns("dim_b"), label = "PCA dimension (y-axis)", min = 1, max = 6, step = 1, value = 2)
             ),
             shiny::div(id = ns("guide_grouping"),
                        labelUI(ns("group")),
@@ -44,7 +44,7 @@ pcaUI <- function(id, show.label = TRUE) {
           shiny::column(
             width = 4,
             shiny::div(id = ns("guide_pointsize"),
-                       shiny::sliderInput(ns("pointsize"),label = "Point size", min = 0.1, max = 10, value = 2),
+                       shiny::sliderInput(ns("pointsize"), label = "Point size", min = 0.1, max = 10, value = 2),
                        shiny::sliderInput(ns("labelsize"), label = "Label size", min = 1, max = 20, value = 5, round = TRUE)
             ),
             shiny::div(id = ns("guide_color"),
@@ -89,7 +89,7 @@ pcaUI <- function(id, show.label = TRUE) {
 pca <- function(input, output, session, clarion, width = 28, height = 28, ppi = 72, scale = 1) {
   # globals/ initialization #####
   # clear plot
-  clearPlot <- shiny::reactiveVal(value = FALSE)
+  clear_plot <- shiny::reactiveVal(value = FALSE)
   # disable downloadButton on init
   shinyjs::disable("download")
   # disable plot button on init
@@ -101,11 +101,11 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
     if (shiny::is.reactive(clarion)) {
       if (!methods::is(clarion(), "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-      obj <- clarion()$clone(deep = TRUE)
+      clarion()$clone(deep = TRUE)
     } else {
       if (!methods::is(clarion, "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-      obj <- clarion$clone(deep = TRUE)
+      clarion$clone(deep = TRUE)
     }
   })
 
@@ -133,21 +133,21 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
   })
 
   # modules/ ui #####
-  columnSelect <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
-  factor_data <- shiny::callModule(label, "group", label = "Select color grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columnSelect$selectedColumns(), !"key"]), unique = FALSE)
-  factor_data2 <- shiny::callModule(label, "group2", label = "Select shape grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columnSelect$selectedColumns(), !"key"]), unique = FALSE)
-  colorPicker <- shiny::callModule(colorPicker, "colorPicker",  distribution = "categorical", selected = "Dark2")
+  columns <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), column.type.label = "Column types to choose from")
+  factor_data <- shiny::callModule(label, "group", label = "Select color grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columns$selected_columns(), !"key"]), unique = FALSE)
+  factor_data2 <- shiny::callModule(label, "group2", label = "Select shape grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columns$selected_columns(), !"key"]), unique = FALSE)
+  color <- shiny::callModule(colorPicker, "colorPicker",  distribution = "categorical", selected = "Dark2")
 
   # update dimension inputs
   shiny::observe({
-    col_num <- length(shiny::req(columnSelect$selectedColumns()))
+    col_num <- length(shiny::req(columns$selected_columns()))
 
     if (col_num >= 3) {
-      valueA <- ifelse(col_num <= input$dimA, col_num - 1, input$dimA)
-      valueB <- ifelse(col_num <= input$dimB, col_num - 1, input$dimB)
+      value_a <- ifelse(col_num <= input$dim_a, col_num - 1, input$dim_a)
+      value_b <- ifelse(col_num <= input$dim_b, col_num - 1, input$dim_b)
 
-      shiny::updateNumericInput(session = session, inputId = "dimA", max = col_num - 1, value = valueA)
-      shiny::updateNumericInput(session = session, inputId = "dimB", max = col_num - 1, value = valueB)
+      shiny::updateNumericInput(session = session, inputId = "dim_a", max = col_num - 1, value = value_a)
+      shiny::updateNumericInput(session = session, inputId = "dim_b", max = col_num - 1, value = value_b)
     }
   })
 
@@ -157,15 +157,15 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
     log_message("PCA: reset", "INFO", token = session$token)
 
     shinyjs::reset("label")
-    shinyjs::reset("dimA")
-    shinyjs::reset("dimB")
+    shinyjs::reset("dim_a")
+    shinyjs::reset("dim_b")
     shinyjs::reset("pointsize")
     shinyjs::reset("labelsize")
-    columnSelect <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column types to choose from")
-    factor_data <<- shiny::callModule(label, "group", label = "Select color grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columnSelect$selectedColumns(), !"key"]), unique = FALSE)
-    factor_data2 <<- shiny::callModule(label, "group2", label = "Select shape grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columnSelect$selectedColumns(), !"key"]), unique = FALSE)
-    colorPicker <<- shiny::callModule(colorPicker, "colorPicker",  distribution = "categorical", selected = "Dark2")
-    clearPlot(TRUE)
+    columns <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), column.type.label = "Column types to choose from")
+    factor_data <<- shiny::callModule(label, "group", label = "Select color grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columns$selected_columns(), !"key"]), unique = FALSE)
+    factor_data2 <<- shiny::callModule(label, "group2", label = "Select shape grouping factors", data = shiny::reactive(object()$get_factors()[key %in% columns$selected_columns(), !"key"]), unique = FALSE)
+    color <<- shiny::callModule(colorPicker, "colorPicker",  distribution = "categorical", selected = "Dark2")
+    clear_plot(TRUE)
   })
 
   result_data <- shiny::reactive({
@@ -174,7 +174,7 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
     on.exit(progress$close())
     progress$set(0.2, message = "Select data")
 
-    selected <- object()$data[, c(object()$get_uniqueID(), columnSelect$selectedColumns()), with = FALSE]
+    selected <- object()$data[, c(object()$get_id(), columns$selected_columns()), with = FALSE]
 
     progress$set(1)
 
@@ -186,7 +186,7 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
 
     # enable downloadButton
     shinyjs::enable("download")
-    clearPlot(FALSE)
+    clear_plot(FALSE)
 
     #new progress indicator
     progress <- shiny::Progress$new()
@@ -197,16 +197,16 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
                data = result_data(),
                color.group = factor_data()$label,
                color.title = paste0(factor_data()$selected, collapse = ", "),
-               palette = colorPicker()$palette,
+               palette = color()$palette,
                shape.group = factor_data2()$label,
                shape.title = paste0(factor_data2()$selected, collapse = ", "),
-               dimensionA = input$dimA,
-               dimensionB = input$dimB,
-               dimensions = length(columnSelect$selectedColumns()) - 1,
+               dimension.a = input$dim_a,
+               dimension.b = input$dim_b,
+               dimensions = length(columns$selected_columns()) - 1,
                pointsize = input$pointsize,
                labelsize = input$labelsize,
                labels = input$label,
-               custom.labels = columnSelect$label(),
+               custom.labels = columns$label(),
                on.columns = TRUE,
                width = size()$width,
                height = size()$height,
@@ -238,7 +238,7 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
     width = plot_width,
     height = plot_height,
     {
-      if (clearPlot()) {
+      if (clear_plot()) {
         return()
       } else {
         log_message("PCA: render plot", "INFO", token = session$token)
@@ -266,8 +266,8 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
   user_input <- shiny::reactive({
     # format selection
     selection <- list(
-      data = list(type = columnSelect$type(), selectedColumns = columnSelect$selectedColumns()),
-      dimensions = list(xaxis = input$dimA, yaxis = input$dimB),
+      data = list(type = columns$type(), selectedColumns = columns$selected_columns()),
+      dimensions = list(xaxis = input$dim_a, yaxis = input$dim_b),
       colorGrouping = factor_data()$selected,
       shapeGrouping = factor_data2()$selected
     )
@@ -277,11 +277,11 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
       show_label = input$label,
       pointsize = input$pointsize,
       labelsize = input$labelsize,
-      colorOptions = list(scheme = colorPicker()$name, reverse = colorPicker()$reverse)
+      colorOptions = list(scheme = color()$name, reverse = color()$reverse)
     )
 
     # merge all
-    all <- list(selection = selection, options = options)
+    list(selection = selection, options = options)
   })
 
   # notifications #####
@@ -291,10 +291,10 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
     shinyjs::enable("plot")
 
     # no selection
-    if (!shiny::isTruthy(columnSelect$selectedColumns())) {
+    if (!shiny::isTruthy(columns$selected_columns())) {
       shinyjs::disable("plot")
     } else {
-      col_num <- length(columnSelect$selectedColumns())
+      col_num <- length(columns$selected_columns())
       # insufficient data
       if (col_num < 3 || nrow(shiny::isolate(object()$data)) < 3) {
         shinyjs::disable("plot")
@@ -308,7 +308,7 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
       }
 
       # invalid dimension
-      if (col_num >= 3 && (is.na(input$dimA) || is.na(input$dimB) || input$dimA <= 0 || input$dimA >= col_num || input$dimB <= 0 || input$dimB >= col_num)) {
+      if (col_num >= 3 && (is.na(input$dim_a) || is.na(input$dim_b) || input$dim_a <= 0 || input$dim_a >= col_num || input$dim_b <= 0 || input$dim_b >= col_num)) {
         shinyjs::disable("plot")
         shiny::showNotification(
           ui = "Invalid dimension(s)! Please select an integer value between 1 and number of selected columns - 1.",

From b6e430202ec9ebb92e30e5bba8dbb1f337c03601 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 13:44:59 +0200
Subject: [PATCH 66/75] lint scatterPlot + example

---
 R/scatterPlot.R            | 234 ++++++++++++++++++-------------------
 exec/scatterPlot_example.R |   2 +-
 man/scatterPlot.Rd         |   4 +-
 3 files changed, 118 insertions(+), 122 deletions(-)

diff --git a/R/scatterPlot.R b/R/scatterPlot.R
index 99e1da8..19c4127 100644
--- a/R/scatterPlot.R
+++ b/R/scatterPlot.R
@@ -117,7 +117,7 @@ scatterPlotUI <- function(id) {
 #' @param output Shiny's output object
 #' @param session Shiny's session object
 #' @param clarion A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)
-#' @param markerOutput Marker module output. See \code{\link[wilson]{marker}}.
+#' @param marker.output Marker module output. See \code{\link[wilson]{marker}}.
 #' @param plot.method Choose to rather render a 'interactive' or 'static' plot. Defaults to 'static'.
 #' @param width Width of the plot in cm. Defaults to minimal size for readable labels and supports reactive.
 #' @param height Height of the plot in cm. Defaults to minimal size for readable labels and supports reactive.
@@ -130,10 +130,10 @@ scatterPlotUI <- function(id) {
 #' @details Intersections between marker and clarion will be removed from clarion in favor of highlighting them.
 #'
 #' @export
-scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, plot.method = "static", width = "auto", height = "auto", ppi = 72, scale = 1) {
+scatterPlot <- function(input, output, session, clarion, marker.output = NULL, plot.method = "static", width = "auto", height = "auto", ppi = 72, scale = 1) {
   # globals/ initialization #####
   # clear plot
-  clearPlot <- shiny::reactiveVal(FALSE)
+  clear_plot <- shiny::reactiveVal(FALSE)
   # disable downloadbutton on init
   shinyjs::disable("download")
   # set labelsize default for interactive
@@ -145,17 +145,17 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
     if (shiny::is.reactive(clarion)) {
       if (!methods::is(clarion(), "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-      obj <- clarion()$clone(deep = TRUE)
+      clarion()$clone(deep = TRUE)
     } else {
       if (!methods::is(clarion, "Clarion")) shiny::stopApp("Object of class 'Clarion' needed!")
 
-      obj <- clarion$clone(deep = TRUE)
+      clarion$clone(deep = TRUE)
     }
   })
   # create deep copy of marker data if existing
-  if (!is.null(markerOutput)) {
+  if (!is.null(marker.output)) {
     marker_object <- shiny::reactive({
-      markerOutput$clarion()$clone(deep = TRUE)
+      marker.output$clarion()$clone(deep = TRUE)
     })
   }
 
@@ -183,20 +183,20 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
   })
 
   # modules/ ui #####
-  xaxis <- shiny::callModule(columnSelector, "xaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_x$method()))
-  yaxis <- shiny::callModule(columnSelector, "yaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_y$method()))
-  zaxis <- shiny::callModule(columnSelector, "zaxis", type.columns = shiny::reactive(object()$metadata[, intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", labelLabel = "Color label", multiple = FALSE, none = TRUE)
-  colorPicker <- shiny::callModule(colorPicker, "color", distribution = "all", winsorize = shiny::reactive(switch(shiny::isTruthy(zaxis$selectedColumn()) + 1, NULL, equalize(object()$data[, zaxis$selectedColumn(), with = FALSE]))))
-  transform_x <- shiny::callModule(transformation, "transform_x", data = shiny::reactive(as.matrix(object()$data[, xaxis$selectedColumn(), with = FALSE])))
-  transform_y <- shiny::callModule(transformation, "transform_y", data = shiny::reactive(as.matrix(object()$data[, yaxis$selectedColumn(), with = FALSE])))
+  xaxis <- shiny::callModule(columnSelector, "xaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), column.type.label = "Column type to choose from", label.label = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_x$method()))
+  yaxis <- shiny::callModule(columnSelector, "yaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), column.type.label = "Column type to choose from", label.label = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_y$method()))
+  zaxis <- shiny::callModule(columnSelector, "zaxis", type.columns = shiny::reactive(object()$metadata[, intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), column.type.label = "Column type to choose from", label.label = "Color label", multiple = FALSE, none = TRUE)
+  color <- shiny::callModule(colorPicker, "color", distribution = "all", winsorize = shiny::reactive(switch(shiny::isTruthy(zaxis$selected_column()) + 1, NULL, equalize(object()$data[, zaxis$selected_column(), with = FALSE]))))
+  transform_x <- shiny::callModule(transformation, "transform_x", data = shiny::reactive(as.matrix(object()$data[, xaxis$selected_column(), with = FALSE])))
+  transform_y <- shiny::callModule(transformation, "transform_y", data = shiny::reactive(as.matrix(object()$data[, yaxis$selected_column(), with = FALSE])))
   # transform highlight data
-  if (!is.null(markerOutput)) {
+  if (!is.null(marker.output)) {
     # note: same id as transform_x/y so it depends on same ui
-    highlight_transform_x <- shiny::callModule(transformation, "transform_x", data = shiny::reactive(as.matrix(marker_object()$data[, xaxis$selectedColumn(), with = FALSE])))
-    highlight_transform_y <- shiny::callModule(transformation, "transform_y", data = shiny::reactive(as.matrix(marker_object()$data[, yaxis$selectedColumn(), with = FALSE])))
+    highlight_transform_x <- shiny::callModule(transformation, "transform_x", data = shiny::reactive(as.matrix(marker_object()$data[, xaxis$selected_column(), with = FALSE])))
+    highlight_transform_y <- shiny::callModule(transformation, "transform_y", data = shiny::reactive(as.matrix(marker_object()$data[, yaxis$selected_column(), with = FALSE])))
   }
-  limit_x <- shiny::callModule(limit, "xaxis_limit", lower = shiny::reactive(result.data()$xlim[1]), upper = shiny::reactive(result.data()$xlim[2]))
-  limit_y <- shiny::callModule(limit, "yaxis_limit", lower = shiny::reactive(result.data()$ylim[1]), upper = shiny::reactive(result.data()$ylim[2]))
+  limit_x <- shiny::callModule(limit, "xaxis_limit", lower = shiny::reactive(result_data()$xlim[1]), upper = shiny::reactive(result_data()$xlim[2]))
+  limit_y <- shiny::callModule(limit, "yaxis_limit", lower = shiny::reactive(result_data()$ylim[1]), upper = shiny::reactive(result_data()$ylim[2]))
 
   # select container dependend on plot.method
   if (plot.method == "static") {
@@ -219,26 +219,26 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
     shinyjs::reset("pointsize")
     shinyjs::reset("labelsize")
     shinyjs::reset("force_cat")
-    xaxis <<- shiny::callModule(columnSelector, "xaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_x$method()))
-    yaxis <<- shiny::callModule(columnSelector, "yaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", labelLabel = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_y$method()))
-    zaxis <<- shiny::callModule(columnSelector, "zaxis", type.columns = shiny::reactive(object()$metadata[, intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), columnTypeLabel = "Column type to choose from", multiple = FALSE, none = TRUE)
-    colorPicker <<- shiny::callModule(colorPicker, "color", distribution = "all", winsorize = shiny::reactive(switch(shiny::isTruthy(zaxis$selectedColumn()) + 1, NULL, equalize(object()$data[, zaxis$selectedColumn(), with = FALSE]))))
-    transform_x <<- shiny::callModule(transformation, "transform_x", data = shiny::reactive(as.matrix(object()$data[, xaxis$selectedColumn(), with = FALSE])))
-    transform_y <<- shiny::callModule(transformation, "transform_y", data = shiny::reactive(as.matrix(object()$data[, yaxis$selectedColumn(), with = FALSE])))
+    xaxis <<- shiny::callModule(columnSelector, "xaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), column.type.label = "Column type to choose from", label.label = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_x$method()))
+    yaxis <<- shiny::callModule(columnSelector, "yaxis", type.columns = shiny::reactive(object()$metadata[level != "feature", intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), column.type.label = "Column type to choose from", label.label = "Axis label", multiple = FALSE, suffix = shiny::reactive(transform_y$method()))
+    zaxis <<- shiny::callModule(columnSelector, "zaxis", type.columns = shiny::reactive(object()$metadata[, intersect(names(object()$metadata), c("key", "level", "label", "sub_label")), with = FALSE]), column.type.label = "Column type to choose from", label.label = "Color label", multiple = FALSE, none = TRUE)
+    color <<- shiny::callModule(colorPicker, "color", distribution = "all", winsorize = shiny::reactive(switch(shiny::isTruthy(zaxis$selected_column()) + 1, NULL, equalize(object()$data[, zaxis$selected_column(), with = FALSE]))))
+    transform_x <<- shiny::callModule(transformation, "transform_x", data = shiny::reactive(as.matrix(object()$data[, xaxis$selected_column(), with = FALSE])))
+    transform_y <<- shiny::callModule(transformation, "transform_y", data = shiny::reactive(as.matrix(object()$data[, yaxis$selected_column(), with = FALSE])))
     # transform highlight data
-    if (!is.null(markerOutput)) {
+    if (!is.null(marker.output)) {
       # note: same id as transform_x/y so it depends on same ui
-      highlight_transform_x <<- shiny::callModule(transformation, "transform_x", data = shiny::reactive(as.matrix(marker_object()$data[, xaxis$selectedColumn(), with = FALSE])))
-      highlight_transform_y <<- shiny::callModule(transformation, "transform_y", data = shiny::reactive(as.matrix(marker_object()$data[, yaxis$selectedColumn(), with = FALSE])))
+      highlight_transform_x <<- shiny::callModule(transformation, "transform_x", data = shiny::reactive(as.matrix(marker_object()$data[, xaxis$selected_column(), with = FALSE])))
+      highlight_transform_y <<- shiny::callModule(transformation, "transform_y", data = shiny::reactive(as.matrix(marker_object()$data[, yaxis$selected_column(), with = FALSE])))
     }
-    limit_x <<- shiny::callModule(limit, "xaxis_limit", lower = shiny::reactive(result.data()$xlim[1]), upper = shiny::reactive(result.data()$xlim[2]))
-    limit_y <<- shiny::callModule(limit, "yaxis_limit", lower = shiny::reactive(result.data()$ylim[1]), upper = shiny::reactive(result.data()$ylim[2]))
-    clearPlot(TRUE)
+    limit_x <<- shiny::callModule(limit, "xaxis_limit", lower = shiny::reactive(result_data()$xlim[1]), upper = shiny::reactive(result_data()$xlim[2]))
+    limit_y <<- shiny::callModule(limit, "yaxis_limit", lower = shiny::reactive(result_data()$ylim[1]), upper = shiny::reactive(result_data()$ylim[2]))
+    clear_plot(TRUE)
   })
 
   # disable plot if mandatory x- or y-axis missing
   shiny::observe({
-    if (!shiny::isTruthy(xaxis$selectedColumn()) || !shiny::isTruthy(yaxis$selectedColumn())) {
+    if (!shiny::isTruthy(xaxis$selected_column()) || !shiny::isTruthy(yaxis$selected_column())) {
       shinyjs::disable("plot")
     } else {
       shinyjs::enable("plot")
@@ -248,85 +248,81 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
   transformed_data <- shiny::reactive({
     # reassemble after transformation
     # columns: unique_id, x, y(, z)
-    if (shiny::isTruthy(zaxis$selectedColumn())) {
-      z <- object()$data[, zaxis$selectedColumn(), with = FALSE]
-      pre.data <- data.table::data.table(object()$data[, object()$get_uniqueID(), with = FALSE], transform_x$data(), transform_y$data(), z)
+    if (shiny::isTruthy(zaxis$selected_column())) {
+      z <- object()$data[, zaxis$selected_column(), with = FALSE]
+      data.table::data.table(object()$data[, object()$get_id(), with = FALSE], transform_x$data(), transform_y$data(), z)
     } else {
-      pre.data <- data.table::data.table(object()$data[, object()$get_uniqueID(), with = FALSE], transform_x$data(), transform_y$data())
+      data.table::data.table(object()$data[, object()$get_id(), with = FALSE], transform_x$data(), transform_y$data())
     }
-
-    return(pre.data)
   })
 
-  if (!is.null(markerOutput)) {
+  if (!is.null(marker.output)) {
     highlight_data <- shiny::reactive({
       # return null on empty table
-      if (nrow(markerOutput$clarion()$data) == 0) return()
+      if (nrow(marker.output$clarion()$data) == 0) return()
       # reassemble after transformation
       # columns: unique_id, x, y(, z)
-      if (shiny::isTruthy(zaxis$selectedColumn())) {
-        z <- marker_object()$data[, zaxis$selectedColumn(), with = FALSE]
-        pre.data <- data.table::data.table(marker_object()$data[, marker_object()$get_uniqueID(), with = FALSE], highlight_transform_x$data(), highlight_transform_y$data(), z)
+      if (shiny::isTruthy(zaxis$selected_column())) {
+        z <- marker_object()$data[, zaxis$selected_column(), with = FALSE]
+        data.table::data.table(marker_object()$data[, marker_object()$get_id(), with = FALSE], highlight_transform_x$data(), highlight_transform_y$data(), z)
       } else {
-        pre.data <- data.table::data.table(marker_object()$data[, marker_object()$get_uniqueID(), with = FALSE], highlight_transform_x$data(), highlight_transform_y$data())
+        data.table::data.table(marker_object()$data[, marker_object()$get_id(), with = FALSE], highlight_transform_x$data(), highlight_transform_y$data())
       }
-
-      return(pre.data)
     })
   }
 
-  result.data <- shiny::eventReactive(input$plot, {
+  result_data <- shiny::eventReactive(input$plot, {
     # new progress indicator
     progress <- shiny::Progress$new()
     on.exit(progress$close())
     progress$set(0, message = "Computing data")
 
     result <- list(
-      processed.data = NULL,
-      data.label = NULL,
-      data.hovertext = NULL,
-      highlight.color = NULL,
-      highlight.label = NULL,
-      highlight.hovertext = NULL,
-      highlight.data = NULL,
+      processed_data = NULL,
+      data_label = NULL,
+      data_hovertext = NULL,
+      highlight_color = NULL,
+      highlight_label = NULL,
+      highlight_hovertext = NULL,
+      highlight_data = NULL,
       xlim = NULL,
       ylim = NULL
     )
 
     # get selected data
     progress$set(0.3, detail = "transforming")
-    processed.data <- transformed_data()
+    processed_data <- transformed_data()
     progress$set(0.5, detail = "selecting")
 
     # no highlighting either disabled or N/A
-    if (is.null(markerOutput) || is.null(highlight_data()) || markerOutput$highlight() == "Disabled") {
+    if (is.null(marker.output) || is.null(highlight_data()) || marker.output$highlight() == "Disabled") {
       # get axis limits
-      result$xlim <- c(min(processed.data[, 2], na.rm = TRUE), max(processed.data[, 2], na.rm = TRUE))
-      result$ylim <- c(min(processed.data[, 3], na.rm = TRUE), max(processed.data[, 3], na.rm = TRUE))
+      result$xlim <- c(min(processed_data[, 2], na.rm = TRUE), max(processed_data[, 2], na.rm = TRUE))
+      result$ylim <- c(min(processed_data[, 3], na.rm = TRUE), max(processed_data[, 3], na.rm = TRUE))
 
       # add name to hovertext
-      if (plot.method == "interactive" && object()$get_name() != object()$get_uniqueID()) {
-        result$data.hovertext <- object()$data[[object()$get_name()]]
+      if (plot.method == "interactive" && object()$get_name() != object()$get_id()) {
+        result$data_hovertext <- object()$data[[object()$get_name()]]
       }
 
-      result$processed.data <- processed.data
+      result$processed_data <- processed_data
     } else {
       # get highlight data
-      highlight.data <- highlight_data()
+      highlight_data <- highlight_data()
 
       # get axis limit including both datasets
-      result$xlim <- c(min(processed.data[, 2], highlight.data[, 2], na.rm = TRUE), max(processed.data[, 2], highlight.data[, 2], na.rm = TRUE))
-      result$ylim <- c(min(processed.data[, 3], highlight.data[, 3], na.rm = TRUE), max(processed.data[, 3], highlight.data[, 3], na.rm = TRUE))
+      result$xlim <- c(min(processed_data[, 2], highlight_data[, 2], na.rm = TRUE), max(processed_data[, 2], highlight_data[, 2], na.rm = TRUE))
+      result$ylim <- c(min(processed_data[, 3], highlight_data[, 3], na.rm = TRUE), max(processed_data[, 3], highlight_data[, 3], na.rm = TRUE))
 
       # get colors
-      result$highlight.color <- markerOutput$color()
+      result$highlight_color <- marker.output$color()
 
-      if (markerOutput$highlight() == "Highlight") {
+      if (marker.output$highlight() == "Highlight") {
         # omit duplicates from processed.data
-        processed.data <- data.table::fsetdiff(x = processed.data, y = highlight.data)
+        processed_data <- data.table::fsetdiff(x = processed_data, y = highlight_data)
 
         # for everything duplicated = empty processed.data
-        if (nrow(processed.data) == 0) {
+        if (nrow(processed_data) == 0) {
           # notification that highlight color will be ignored
           shiny::showNotification(
             id = session$ns("full_highlight"),
@@ -338,45 +334,45 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
           shinyjs::runjs(paste0("$(document.getElementById('", paste0("shiny-notification-", session$ns("full_highlight")), "')).addClass('notification-position-center');"))
 
           # add name to hovertext
-          if (plot.method == "interactive" && marker_object()$get_name() != marker_object()$get_uniqueID()) {
-            result$data.hovertext <- marker_object()$data[[marker_object()$get_name()]]
+          if (plot.method == "interactive" && marker_object()$get_name() != marker_object()$get_id()) {
+            result$data_hovertext <- marker_object()$data[[marker_object()$get_name()]]
           }
 
-          result$processed.data <- highlight.data
+          result$processed_data <- highlight_data
         } else {
           # add name to hovertext
-          if (plot.method == "interactive" && object()$get_name() != object()$get_uniqueID()) {
+          if (plot.method == "interactive" && object()$get_name() != object()$get_id()) {
             # only keep selected rows
-            result$data.hovertext <- object()$data[processed.data, on = object()$get_uniqueID()][[object()$get_name()]]
+            result$data_hovertext <- object()$data[processed_data, on = object()$get_id()][[object()$get_name()]]
           }
           # add name to hovertext
-          if (plot.method == "interactive" && marker_object()$get_name() != marker_object()$get_uniqueID()) {
-            result$highlight.hovertext <- marker_object()$data[[marker_object()$get_name()]]
+          if (plot.method == "interactive" && marker_object()$get_name() != marker_object()$get_id()) {
+            result$highlight_hovertext <- marker_object()$data[[marker_object()$get_name()]]
           }
 
-          result$processed.data <- processed.data
-          result$highlight.data <- highlight.data
+          result$processed_data <- processed_data
+          result$highlight_data <- highlight_data
         }
 
         # set label; ignore if more than 100
-        if (length(markerOutput$label()) <= 100) {
-          if (nrow(processed.data) == 0) {
-            result$data.label <- markerOutput$label()
+        if (length(marker.output$label()) <= 100) {
+          if (nrow(processed_data) == 0) {
+            result$data_label <- marker.output$label()
           } else {
-            result$highlight.label <- markerOutput$label()
+            result$highlight_label <- marker.output$label()
           }
         }
-      } else if (markerOutput$highlight() == "Exclusive") {
+      } else if (marker.output$highlight() == "Exclusive") {
         # add name to hovertext
-        if (plot.method == "interactive" && marker_object()$get_name() != marker_object()$get_uniqueID()) {
+        if (plot.method == "interactive" && marker_object()$get_name() != marker_object()$get_id()) {
           result$data.hovertext <- marker_object()$data[[marker_object()$get_name()]]
         }
 
-        result$processed.data <- highlight.data
+        result$processed_data <- highlight_data
 
         # set label; ignore if more than 100
-        if (length(markerOutput$label()) <= 100) {
-          result$data.label <- markerOutput$label()
+        if (length(marker.output$label()) <= 100) {
+          result$data_label <- marker.output$label()
         }
       }
     }
@@ -390,7 +386,7 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
 
     # enable downloadbutton
     shinyjs::enable("download")
-    clearPlot(FALSE)
+    clear_plot(FALSE)
 
     # new progress indicator
     progress <- shiny::Progress$new()
@@ -400,40 +396,40 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
     if (!is.null(limit_x())) {
       xlimit <- unlist(limit_x())
     } else {
-      xlimit <- result.data()$xlim
+      xlimit <- result_data()$xlim
     }
     if (!is.null(limit_y())) {
       ylimit <- unlist(limit_y())
     } else {
-      ylimit <- result.data()$ylim
+      ylimit <- result_data()$ylim
     }
 
     plot <- create_scatterplot(
-      data = result.data()$processed.data,
-      data.labels = result.data()$data.label,
-      data.hovertext <- result.data()$data.hovertext,
-      color = colorPicker()$palette,
+      data = result_data()$processed_data,
+      data.labels = result_data()$data_label,
+      data.hovertext <- result_data()$data_hovertext,
+      color = color()$palette,
       x_label = xaxis$label(),
       y_label = yaxis$label(),
       z_label = zaxis$label(),
-      transparency = colorPicker()$transparency,
+      transparency = color()$transparency,
       pointsize = input$pointsize,
       labelsize = input$labelsize,
       density = input$density,
       line = input$line,
-      highlight.data = result.data()$highlight.data,
-      highlight.color = result.data()$highlight.color,
-      highlight.labels = result.data()$highlight.label,
-      highlight.hovertext = result.data()$highlight.hovertext,
+      highlight.data = result_data()$highlight_data,
+      highlight.color = result_data()$highlight_color,
+      highlight.labels = result_data()$highlight_label,
+      highlight.hovertext = result_data()$highlight_hovertext,
       xlim = xlimit,
       ylim = ylimit,
-      colorbar.limits = colorPicker()$winsorize,
+      colorbar.limits = color()$winsorize,
       plot.method = plot.method,
       width = size()$width,
       height = size()$height,
       ppi = size()$ppi,
       scale = size()$scale,
-      categorized = if (input$force_cat || ncol(result.data()$processed.data) >= 4 && !is.numeric(result.data()$processed.data[[4]])) TRUE else FALSE
+      categorized = if (input$force_cat || ncol(result_data()$processed_data) >= 4 && !is.numeric(result_data()$processed_data[[4]])) TRUE else FALSE
     )
 
     progress$set(1)
@@ -447,7 +443,7 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
       width = shiny::reactive(plot()$width * (plot()$ppi / 2.54)),
       height = shiny::reactive(plot()$height * (plot()$ppi / 2.54)),
       {
-        if (clearPlot()) {
+        if (clear_plot()) {
           return()
         } else {
           log_message("Scatterplot: render plot static", "INFO", token = session$token)
@@ -458,7 +454,7 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
     )
   } else if (plot.method == "interactive") {
     output$interactive <- plotly::renderPlotly({
-      if (clearPlot()) {
+      if (clear_plot()) {
         return()
       } else {
         log_message("Scatterplot: render plot interactive", "INFO", token = session$token)
@@ -497,10 +493,10 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
 
     # format appearance
     appearance <- list(
-      scheme = colorPicker()$name,
-      reverse = colorPicker()$reverse,
-      winsorize = colorPicker()$winsorize,
-      transparency = colorPicker()$transparency,
+      scheme = color()$name,
+      reverse = color()$reverse,
+      winsorize = color()$winsorize,
+      transparency = color()$transparency,
       pointsize = input$pointsize,
       labelsize = input$labelsize)
 
@@ -509,27 +505,27 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
 
     # format marker
     marker <- NULL
-    if (!is.null(markerOutput)) {
+    if (!is.null(marker.output)) {
       marker <- list(
-        highlight = markerOutput$highlight(),
-        color = markerOutput$color(),
-        labelColumn = markerOutput$labelColumn(),
-        label = markerOutput$label()
+        highlight = marker.output$highlight(),
+        color = marker.output$color(),
+        label_column = marker.output$label_column(),
+        label = marker.output$label()
       )
     }
 
     # merge all
-    all <- list(axis = axis, appearance = appearance, options = options, marker = marker)
+    list(axis = axis, appearance = appearance, options = options, marker = marker)
   })
 
   # notifications #####
   # show warning if there would be more than 10 categories
   shiny::observe({
     # something selected?
-    if (shiny::isTruthy(zaxis$selectedColumn())) {
+    if (shiny::isTruthy(zaxis$selected_column())) {
       # categories used?
-      if (input$force_cat || !is.numeric(object()$data[[zaxis$selectedColumn()]])) {
-        cat_num <- length(unique(object()$data[[zaxis$selectedColumn()]]))
+      if (input$force_cat || !is.numeric(object()$data[[zaxis$selected_column()]])) {
+        cat_num <- length(unique(object()$data[[zaxis$selected_column()]]))
 
         if (cat_num > 10) {
           shiny::showNotification(
@@ -565,12 +561,12 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
   })
 
   # label restriction warning
-  if (!is.null(markerOutput)) {
+  if (!is.null(marker.output)) {
     shiny::observe({
-      if (markerOutput$highlight() != "Disabled" && length(markerOutput$label()) > 100) {
+      if (marker.output$highlight() != "Disabled" && length(marker.output$label()) > 100) {
         shiny::showNotification(
           id = session$ns("label-limit"),
-          paste("Warning! Label restricted to 100 or less labels. Currently selected:", length(markerOutput$label()), "Please select fewer genes to label or else they will be ignored."),
+          paste("Warning! Label restricted to 100 or less labels. Currently selected:", length(marker.output$label()), "Please select fewer genes to label or else they will be ignored."),
           duration = NULL,
           type = "warning"
         )
@@ -582,12 +578,12 @@ scatterPlot <- function(input, output, session, clarion, markerOutput = NULL, pl
   }
 
   # Fetch the reactive guide for this module
-  guide <- scatterPlotGuide(session, !is.null(markerOutput))
+  guide <- scatterPlotGuide(session, !is.null(marker.output))
   shiny::observeEvent(input$guide, {
     rintrojs::introjs(session, options = list(steps = guide()))
   })
 
-  return(shiny::reactive({unique(data.table::rbindlist(list(result.data()$processed.data, result.data()$highlight.data)))}))
+  return(shiny::reactive({unique(data.table::rbindlist(list(result_data()$processed_data, result_data()$highlight_data)))}))
 }
 
 #' scatterPlot module guide
diff --git a/exec/scatterPlot_example.R b/exec/scatterPlot_example.R
index df336c6..e18482d 100644
--- a/exec/scatterPlot_example.R
+++ b/exec/scatterPlot_example.R
@@ -39,7 +39,7 @@ server <- function(input, output) {
   marked <- Clarion$new(metadata = metadata, data = data[1:10])
   marker <- callModule(marker, "marker", clarion = marked)
 
-  plot <- callModule(scatterPlot, "id", clarion = clarion, markerOutput = marker, plot.method = "interactive", width = reactive(input$width), height = reactive(input$height), scale = reactive(input$scale))
+  plot <- callModule(scatterPlot, "id", clarion = clarion, marker.output = marker, plot.method = "interactive", width = reactive(input$width), height = reactive(input$height), scale = reactive(input$scale))
 
   observe({
     print(plot())
diff --git a/man/scatterPlot.Rd b/man/scatterPlot.Rd
index 9cb7168..7adce15 100644
--- a/man/scatterPlot.Rd
+++ b/man/scatterPlot.Rd
@@ -4,7 +4,7 @@
 \alias{scatterPlot}
 \title{scatterPlot module server logic}
 \usage{
-scatterPlot(input, output, session, clarion, markerOutput = NULL,
+scatterPlot(input, output, session, clarion, marker.output = NULL,
   plot.method = "static", width = "auto", height = "auto", ppi = 72,
   scale = 1)
 }
@@ -17,7 +17,7 @@ scatterPlot(input, output, session, clarion, markerOutput = NULL,
 
 \item{clarion}{A clarion object. See \code{\link[wilson]{Clarion}}. (Supports reactive)}
 
-\item{markerOutput}{Marker module output. See \code{\link[wilson]{marker}}.}
+\item{marker.output}{Marker module output. See \code{\link[wilson]{marker}}.}
 
 \item{plot.method}{Choose to rather render a 'interactive' or 'static' plot. Defaults to 'static'.}
 

From f938bad12784f5685925b31a3bdd577cad39db6a Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 13:53:33 +0200
Subject: [PATCH 67/75] lint transformation

---
 R/transformation.R | 38 +++++++++++++++++++-------------------
 1 file changed, 19 insertions(+), 19 deletions(-)

diff --git a/R/transformation.R b/R/transformation.R
index 2b7a87c..1266a77 100644
--- a/R/transformation.R
+++ b/R/transformation.R
@@ -16,13 +16,13 @@ transformationUI <- function(id, label = "Transformation", selected = "raw", cho
 
   ret <- list(
     shiny::tags$b(label),
-    #shiny::actionLink(ns("help"), label = NULL, icon = shiny::icon("question-circle")), # removed for now
+    # shiny::actionLink(ns("help"), label = NULL, icon = shiny::icon("question-circle")), # removed for now
     shiny::selectInput(ns("transform"),
                             label = NULL,
                             choices = choices,
                             selected = selected,
                             multiple = F))
-  if(transposeOptions){
+  if (transposeOptions) {
     ret <- list(ret, shinyjs::useShinyjs(), shiny::radioButtons(ns("transpose"), label = NULL, choices = c(`row-wise` = "row", `column-wise` = "column")))
   }
 
@@ -49,20 +49,20 @@ transformationUI <- function(id, label = "Transformation", selected = "raw", cho
 #'
 #' @export
 transformation <- function(input, output, session, data, transpose = FALSE, pseudocount = 1, replaceInf = TRUE, replaceNA = TRUE) {
-  #handle reactive data
-  data.r <- shiny::reactive({
-    if(shiny::is.reactive(data)){
+  # handle reactive data
+  data_r <- shiny::reactive({
+    if (shiny::is.reactive(data)) {
       data()
-    }else{
+    } else {
       data
     }
   })
 
-  #reset
+  # reset
   shinyjs::reset("transform")
   shinyjs::reset("transpose")
 
-  #helptext
+  # helptext
   # shiny::observeEvent(input$help, {
   #   title <- "Data transformation"
   #   content <- shiny::HTML("Choose a method with which the given data is transformed:<br/>")
@@ -109,13 +109,13 @@ transformation <- function(input, output, session, data, transpose = FALSE, pseu
   }
 
   transformed_data <- shiny::reactive({
-    data <- data.r()
+    data <- data_r()
 
-    if(transpose | ifelse(!is.null(input$transpose), input$transpose == "row", FALSE) & input$transform == "zscore"){
+    if (transpose | ifelse(!is.null(input$transpose), input$transpose == "row", FALSE) & input$transform == "zscore") {
       data <- t(data)
     }
 
-    #transform data
+    # transform data
     output <- switch(input$transform,
       log2 = log2(data + pseudocount),
       `-log2` = -log2(data + pseudocount),
@@ -126,32 +126,32 @@ transformation <- function(input, output, session, data, transpose = FALSE, pseu
       raw = data
     )
 
-    #replace infinite with NA & NA with 0
-    if(replaceInf){
+    # replace infinite with NA & NA with 0
+    if (replaceInf) {
       is.na(output) <- sapply(output, is.infinite)
     }
-    if(replaceNA){
+    if (replaceNA) {
       output[is.na(output)] <- 0
     }
 
-    if(transpose | ifelse(!is.null(input$transpose), input$transpose == "row", FALSE) & input$transform == "zscore"){
+    if (transpose | ifelse(!is.null(input$transpose), input$transpose == "row", FALSE) & input$transform == "zscore") {
       output <- t(output)
     }
 
     return(output)
   })
 
-  #enable transposeOptions only if relevant
+  # enable transposeOptions only if relevant
   shiny::observe({
-    if(input$transform == "zscore"){
+    if (input$transform == "zscore") {
       shinyjs::enable("transpose")
-    }else{
+    } else {
       shinyjs::disable("transpose")
     }
   })
 
   method <- shiny::reactive({
-    if(input$transform == "zscore") {
+    if (input$transform == "zscore") {
       paste(input$transform, input$transpose)
     } else {
       input$transform

From 8d41dfddb26b22679356234085b94d00850518f4 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 14:13:43 +0200
Subject: [PATCH 68/75] download: restore wd on exit

---
 R/function.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/function.R b/R/function.R
index 1aed7cf..8152510 100644
--- a/R/function.R
+++ b/R/function.R
@@ -1234,6 +1234,7 @@ download <- function(file, filename, plot, width, height, ppi = 72, save_plot =
     # plotly
     # change working directory temporary so mounted drives are not a problem
     wd <- getwd()
+    on.exit(setwd(wd)) # make sure working directory will be restored
     setwd(tempdir())
     plotly::export(p = plot, file = plot_file_pdf)
     plotly::export(p = plot, file = plot_file_png)

From 63f5ed9ed28df4d6eb6179e7f8cffe7dfe285eee Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 14:23:15 +0200
Subject: [PATCH 69/75] and, featureSelector, function: use less error prone
 seq_len() instead of 1:x

---
 R/and.R             | 6 +++---
 R/featureSelector.R | 2 +-
 R/function.R        | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/and.R b/R/and.R
index 13e8e98..3614a52 100644
--- a/R/and.R
+++ b/R/and.R
@@ -134,7 +134,7 @@ and <- function(input, output, session, data, show.elements = NULL, element.grou
       # keep grouping order
       grouping <- grouping[unique(element.grouping[[2]])]
 
-      return <- lapply(1:length(grouping), function(i){
+      return <- lapply(seq_len(length(grouping)), function(i){
         group <- lapply(unlist(grouping[i]), function(x){
           progress$inc(step, detail = x)
 
@@ -164,7 +164,7 @@ and <- function(input, output, session, data, show.elements = NULL, element.grou
         shiny::tagList(shinydashboard::box(width = 12, collapsible = TRUE, collapsed = TRUE, title = names(grouping[i]), shiny::tagList(group)))
       })
     } else {
-      return <- lapply(1:ncol(data), function(x) {
+      return <- lapply(seq_len(ncol(data)), function(x) {
         progress$inc(step, detail = names(data)[x])
         if (is.numeric(data[[x]])) {
           ui <- orNumericUI(id = session$ns(openssl::sha1(names(data)[x])))
@@ -205,7 +205,7 @@ and <- function(input, output, session, data, show.elements = NULL, element.grou
     progress$set(0, message = "Filtering Module:")
     step <- ncol(data_r())
 
-    lapply(1:ncol(data_r()), function(x) {
+    lapply(seq_len(ncol(data_r())), function(x) {
       progress$inc(step, detail = names(data_r())[x])
       if (is.numeric(data_r()[[x]])) {
         if (parameter()$ranged[x]) {
diff --git a/R/featureSelector.R b/R/featureSelector.R
index 0e2be02..2d9f4ba 100644
--- a/R/featureSelector.R
+++ b/R/featureSelector.R
@@ -99,7 +99,7 @@ featureSelector <- function(input, output, session, clarion, multiple = TRUE, co
   # row_selector choices
   choices <- shiny::reactive({
     if (nrow(data_output()$data) > 0) {
-      c(1:nrow(data_output()$data))
+      seq_len(nrow(data_output()$data))
     } else {
       c(0, 0)
     }
diff --git a/R/function.R b/R/function.R
index 8152510..5506fef 100644
--- a/R/function.R
+++ b/R/function.R
@@ -798,7 +798,7 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
 
   # place former colnames in cols
   data$cols <- data_cols
-  data.table::setcolorder(data, c("cols", colnames(data)[1:ncol(data) - 1]))
+  data.table::setcolorder(data, c("cols", colnames(data)[seq_len(ncol(data)) - 1]))
   # reattach ids as colnames
   names(data)[2:ncol(data)] <- data_id
 

From 117e0c4874912f6c965d601b2ed65a8d58391064 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 14:43:15 +0200
Subject: [PATCH 70/75] T -> TRUE; F -> FALSE

---
 R/columnSelector.R        |  2 +-
 R/function.R              |  2 +-
 R/scatterPlot.R           |  6 +++---
 R/transformation.R        |  2 +-
 man/columnSelectorUI.Rd   |  2 +-
 man/create_scatterplot.Rd | 11 ++++++-----
 6 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/R/columnSelector.R b/R/columnSelector.R
index 0130eff..cf5217e 100644
--- a/R/columnSelector.R
+++ b/R/columnSelector.R
@@ -7,7 +7,7 @@
 #' @return A list from \code{\link[shiny]{tag}} with the UI elements.
 #'
 #' @export
-columnSelectorUI <- function(id, label = F, title = NULL) {
+columnSelectorUI <- function(id, label = FALSE, title = NULL) {
   # create namespace
   ns <- shiny::NS(id)
 
diff --git a/R/function.R b/R/function.R
index 5506fef..41cfc11 100644
--- a/R/function.R
+++ b/R/function.R
@@ -33,7 +33,7 @@
 #' @import data.table
 #'
 #' @return Returns list(plot = ggplotly/ ggplot, width, height, ppi, exceed_size).
-create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL, transparency = 1, pointsize = 1, labelsize = 3, color = NULL, x_label = "", y_label = "", z_label = "", density = T, line = T, categorized = F, highlight.data = NULL, highlight.labels = NULL, highlight.hovertext = NULL, highlight.color = "#FF0000", xlim = NULL, ylim = NULL, colorbar.limits = NULL, width = "auto", height = "auto", ppi = 72, plot.method = "static", scale = 1){
+create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL, transparency = 1, pointsize = 1, labelsize = 3, color = NULL, x_label = "", y_label = "", z_label = "", density = TRUE, line = TRUE, categorized = FALSE, highlight.data = NULL, highlight.labels = NULL, highlight.hovertext = NULL, highlight.color = "#FF0000", xlim = NULL, ylim = NULL, colorbar.limits = NULL, width = "auto", height = "auto", ppi = 72, plot.method = "static", scale = 1){
   # force evaluation of all arguments
   # no promises in plot object
   forceArgs()
diff --git a/R/scatterPlot.R b/R/scatterPlot.R
index 19c4127..950b2ea 100644
--- a/R/scatterPlot.R
+++ b/R/scatterPlot.R
@@ -28,7 +28,7 @@ scatterPlotUI <- function(id) {
                        columnSelectorUI(
                          id = ns("xaxis"),
                          title = "Data on x-axis",
-                         label = T
+                         label = TRUE
                        )
             ),
             shiny::div(id = ns("guide_xaxis_transformation"),
@@ -43,7 +43,7 @@ scatterPlotUI <- function(id) {
                        columnSelectorUI(
                          id = ns("yaxis"),
                          title = "Data on y-axis",
-                         label = T
+                         label = TRUE
                        )
             ),
             shiny::div(id = ns("guide_yaxis_transformation"),
@@ -59,7 +59,7 @@ scatterPlotUI <- function(id) {
                        columnSelectorUI(
                          id = ns("zaxis"),
                          title = "Data on z-axis",
-                         label = T
+                         label = TRUE
                        ),
                        shiny::checkboxInput(
                          inputId = ns("force_cat"),
diff --git a/R/transformation.R b/R/transformation.R
index 1266a77..b535995 100644
--- a/R/transformation.R
+++ b/R/transformation.R
@@ -21,7 +21,7 @@ transformationUI <- function(id, label = "Transformation", selected = "raw", cho
                             label = NULL,
                             choices = choices,
                             selected = selected,
-                            multiple = F))
+                            multiple = FALSE))
   if (transposeOptions) {
     ret <- list(ret, shinyjs::useShinyjs(), shiny::radioButtons(ns("transpose"), label = NULL, choices = c(`row-wise` = "row", `column-wise` = "column")))
   }
diff --git a/man/columnSelectorUI.Rd b/man/columnSelectorUI.Rd
index a81a734..dca9df2 100644
--- a/man/columnSelectorUI.Rd
+++ b/man/columnSelectorUI.Rd
@@ -4,7 +4,7 @@
 \alias{columnSelectorUI}
 \title{columnSelector module UI representation}
 \usage{
-columnSelectorUI(id, label = F, title = NULL)
+columnSelectorUI(id, label = FALSE, title = NULL)
 }
 \arguments{
 \item{id}{The ID of the modules namespace.}
diff --git a/man/create_scatterplot.Rd b/man/create_scatterplot.Rd
index 1e60d4b..d219acd 100644
--- a/man/create_scatterplot.Rd
+++ b/man/create_scatterplot.Rd
@@ -6,11 +6,12 @@
 \usage{
 create_scatterplot(data, data.labels = NULL, data.hovertext = NULL,
   transparency = 1, pointsize = 1, labelsize = 3, color = NULL,
-  x_label = "", y_label = "", z_label = "", density = T, line = T,
-  categorized = F, highlight.data = NULL, highlight.labels = NULL,
-  highlight.hovertext = NULL, highlight.color = "#FF0000", xlim = NULL,
-  ylim = NULL, colorbar.limits = NULL, width = "auto", height = "auto",
-  ppi = 72, plot.method = "static", scale = 1)
+  x_label = "", y_label = "", z_label = "", density = TRUE,
+  line = TRUE, categorized = FALSE, highlight.data = NULL,
+  highlight.labels = NULL, highlight.hovertext = NULL,
+  highlight.color = "#FF0000", xlim = NULL, ylim = NULL,
+  colorbar.limits = NULL, width = "auto", height = "auto", ppi = 72,
+  plot.method = "static", scale = 1)
 }
 \arguments{
 \item{data}{data.table containing plot data

From 45de92b3d0afbfa0d19065c512eadc1763b64344 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Thu, 28 Jun 2018 15:28:09 +0200
Subject: [PATCH 71/75] deleted unused imports

---
 DESCRIPTION | 2 --
 1 file changed, 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e040e15..3342e24 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -34,7 +34,6 @@ Imports: shiny,
     gplots,
     reshape,
     rintrojs,
-    webshot,
     RJSONIO,
     ggrepel (>= 0.6.12),
     DESeq2,
@@ -42,7 +41,6 @@ Imports: shiny,
     FactoMineR,
     factoextra,
     heatmaply (>= 0.14.1),
-    shinythemes,
     shinycssloaders,
     log4r,
     openssl,

From ad9573aea06caccc6b492bef41d4de202d09b870 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 29 Jun 2018 09:00:38 +0200
Subject: [PATCH 72/75] replaced sapply with type safe v- /lapply

---
 R/and.R             | 10 +++-------
 R/clarion.R         |  2 +-
 R/featureSelector.R |  2 +-
 R/function.R        | 10 +++++-----
 R/pca.R             | 10 ++++++++--
 R/transformation.R  |  2 +-
 6 files changed, 19 insertions(+), 17 deletions(-)

diff --git a/R/and.R b/R/and.R
index 3614a52..0d7f889 100644
--- a/R/and.R
+++ b/R/and.R
@@ -260,21 +260,17 @@ and <- function(input, output, session, data, show.elements = NULL, element.grou
 
     step <- 0.9 / length(or_modules)
     # OR modules selection
-    or_selection_bool <- sapply(or_modules, function(x) {
+    or_selection_bool <- vapply(or_modules, FUN.VALUE = logical(nrow(data_r())), FUN = function(x) {
       progress$inc(step, detail = x()$label)
       x()$bool
     })
-    or_selection_text <- sapply(or_modules, function(x) {
+
+    or_selection_text <- lapply(or_modules, function(x) {
       if (shiny::isTruthy(x()$text)) {
         return(paste0(x()$label, ": ", paste(x()$text, collapse = ","), collapse = ""))
       }
     })
 
-    # cast to matrix if sapply returns vector
-    if (is.vector(or_selection_bool)) {
-      or_selection_bool <- t(as.matrix(or_selection_bool))
-    }
-
     # selected rows (and selection)
     and_selection_bool <- apply(or_selection_bool, 1, all)
 
diff --git a/R/clarion.R b/R/clarion.R
index 5c0260d..22ce390 100644
--- a/R/clarion.R
+++ b/R/clarion.R
@@ -245,7 +245,7 @@ Clarion <- R6::R6Class("Clarion",
                            } else {
                              expected_numeric_cols <- self$metadata[level %in% c("sample", "condition", "contrast")][["key"]]
                            }
-                           not_numeric <- names(self$data[, expected_numeric_cols, with = FALSE][, which(!sapply(self$data[, expected_numeric_cols, with = FALSE], is.numeric))])
+                           not_numeric <- names(self$data[, expected_numeric_cols, with = FALSE][, which(!vapply(self$data[, expected_numeric_cols, with = FALSE], is.numeric, FUN.VALUE = logical(1)))])
                            if (length(not_numeric) > 0) {
                              stop("Data: Column(s): ", paste0(not_numeric, collapse = ", "), " not numeric! Probably wrong decimal separator.")
                            }
diff --git a/R/featureSelector.R b/R/featureSelector.R
index 2d9f4ba..40b2bce 100644
--- a/R/featureSelector.R
+++ b/R/featureSelector.R
@@ -83,7 +83,7 @@ featureSelector <- function(input, output, session, clarion, multiple = TRUE, co
   # delimiter vector
   # only delimit type = array
   delimiter <- shiny::reactive({
-    sapply(object()$metadata[["key"]], function(x) {
+    lapply(object()$metadata[["key"]], function(x) {
       if (object()$is_delimited(x)) {
         return(object()$get_delimiter())
       } else {
diff --git a/R/function.R b/R/function.R
index 41cfc11..d93701a 100644
--- a/R/function.R
+++ b/R/function.R
@@ -690,10 +690,10 @@ create_heatmap <- function(data, unitlabel = "auto", row.label = TRUE, row.custo
     ))
 
     # width/ height calculation
-    col_names_maxlength_label_width <- max(sapply(colnames(prep_data), graphics::strwidth, units = "in", font = 12))	# longest column label when plotted in inches
-    col_names_maxlength_label_height <- max(sapply(colnames(prep_data), graphics::strheight, units = "in", font = 12))	# highest column label when plotted in inches
-    row_names_maxlength_label_width <- max(sapply(rownames(prep_data), graphics::strwidth, units = "in", font = 12))	# longest row label when plotted in inches
-    row_names_maxlength_label_height <- max(sapply(rownames(prep_data), graphics::strheight, units = "in", font = 12))	# highest row label when plotted in inches
+    col_names_maxlength_label_width <- max(vapply(colnames(prep_data), FUN.VALUE = numeric(1), graphics::strwidth, units = "in", font = 12))	# longest column label when plotted in inches
+    col_names_maxlength_label_height <- max(vapply(colnames(prep_data), FUN.VALUE = numeric(1), graphics::strheight, units = "in", font = 12))	# highest column label when plotted in inches
+    row_names_maxlength_label_width <- max(vapply(rownames(prep_data), FUN.VALUE = numeric(1), graphics::strwidth, units = "in", font = 12))	# longest row label when plotted in inches
+    row_names_maxlength_label_height <- max(vapply(rownames(prep_data), FUN.VALUE = numeric(1), graphics::strheight, units = "in", font = 12))	# highest row label when plotted in inches
 
     # width
     if (row.label) {
@@ -791,7 +791,7 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
   } else {
     data_id <- gene.label
   }
-  data <- data[, sapply(data, is.numeric), with = FALSE]
+  data <- data[, vapply(data, is.numeric, FUN.VALUE = logical(1)), with = FALSE]
 
   data_cols <- names(data)
   data <- data.table::transpose(data) 								# switch columns <> rows
diff --git a/R/pca.R b/R/pca.R
index 6dade4a..edca112 100644
--- a/R/pca.R
+++ b/R/pca.R
@@ -249,11 +249,17 @@ pca <- function(input, output, session, clarion, width = 28, height = 28, ppi =
 
   # group data by dimension
   reorganized_data <- shiny::reactive({
-    sapply(colnames(plot()$data$var$coord), USE.NAMES = TRUE, simplify = FALSE, function(dim) {
-      sapply(plot()$data$var, function(table) {
+    dims <- lapply(colnames(plot()$data$var$coord), function(dim) {
+      dim_data <- lapply(plot()$data$var, function(table) {
         table[, dim]
       })
+
+      do.call(cbind, dim_data)
     })
+
+    names(dims) <- colnames(plot()$data$var$coord)
+
+    return(dims)
   })
 
   # download #####
diff --git a/R/transformation.R b/R/transformation.R
index b535995..2a13f15 100644
--- a/R/transformation.R
+++ b/R/transformation.R
@@ -128,7 +128,7 @@ transformation <- function(input, output, session, data, transpose = FALSE, pseu
 
     # replace infinite with NA & NA with 0
     if (replaceInf) {
-      is.na(output) <- sapply(output, is.infinite)
+      is.na(output) <- vapply(output, FUN = is.infinite, FUN.VALUE = logical(1))
     }
     if (replaceNA) {
       output[is.na(output)] <- 0

From 670b26f050aab375c345edbf9ceaec6fbda1e69f Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 29 Jun 2018 09:04:42 +0200
Subject: [PATCH 73/75] columnSelector: fixed typo

---
 R/columnSelector.R    | 2 +-
 man/columnSelector.Rd | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/columnSelector.R b/R/columnSelector.R
index cf5217e..fa17e47 100644
--- a/R/columnSelector.R
+++ b/R/columnSelector.R
@@ -31,7 +31,7 @@ columnSelectorUI <- function(id, label = FALSE, title = NULL) {
 #'                                label = optional, used instead of id
 #'                                sub_label = optional, added to id/ label
 #' @param type The type (contrast/group/sample of the type dropdown menu, selected in step 1 (upper dropdown). Defaults to unique(type.columns[,2]) (Supports reactive)
-#' @param column.type.tabel Changes the label of the first UI element
+#' @param column.type.label Changes the label of the first UI element
 #' @param label.label Change label above label text input.
 #' @param multiple Boolean value whether multiple values can be selected in second selector. (Default = TRUE)
 #' @param none If TRUE adds "None to secondSelector and select is. (Default = FALSE)
diff --git a/man/columnSelector.Rd b/man/columnSelector.Rd
index 9ababef..5f08b90 100644
--- a/man/columnSelector.Rd
+++ b/man/columnSelector.Rd
@@ -23,6 +23,8 @@ sub_label = optional, added to id/ label}
 
 \item{type}{The type (contrast/group/sample of the type dropdown menu, selected in step 1 (upper dropdown). Defaults to unique(type.columns[,2]) (Supports reactive)}
 
+\item{column.type.label}{Changes the label of the first UI element}
+
 \item{label.label}{Change label above label text input.}
 
 \item{multiple}{Boolean value whether multiple values can be selected in second selector. (Default = TRUE)}
@@ -32,8 +34,6 @@ sub_label = optional, added to id/ label}
 \item{sep}{Used to separate labels on multi value selection.}
 
 \item{suffix}{Added to label only on multiple = FALSE (supports reactive). Also uses sep as separator.}
-
-\item{column.type.tabel}{Changes the label of the first UI element}
 }
 \value{
 Returns the input. As named list: names("type", "selected_columns", "label")

From 5828ee94c61d23b751cc580cb627be4599d773a1 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 29 Jun 2018 09:57:41 +0200
Subject: [PATCH 74/75] update revdep_check

---
 revdep/README.md   |   6 ++----
 revdep/checks.rds  | Bin 938 -> 911 bytes
 revdep/data.sqlite | Bin 20480 -> 0 bytes
 revdep/problems.md |   6 ++----
 4 files changed, 4 insertions(+), 8 deletions(-)
 delete mode 100644 revdep/data.sqlite

diff --git a/revdep/README.md b/revdep/README.md
index e8c8c48..3b38cae 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -10,7 +10,7 @@
 |language |(EN)                         |
 |collate  |German_Germany.1252          |
 |tz       |Europe/Berlin                |
-|date     |2018-06-27                   |
+|date     |2018-06-29                   |
 
 ## Packages
 
@@ -44,10 +44,8 @@
 |shinycssloaders |   |0.2.0   |2017-05-12 |CRAN (R 3.5.0)                      |
 |shinydashboard  |   |0.7.0   |2018-03-21 |CRAN (R 3.5.0)                      |
 |shinyjs         |   |1.0     |2018-01-08 |CRAN (R 3.5.0)                      |
-|shinythemes     |   |1.1.1   |2016-10-12 |CRAN (R 3.5.0)                      |
 |viridis         |   |0.5.1   |2018-03-29 |CRAN (R 3.5.0)                      |
-|webshot         |   |0.5.0   |2017-11-29 |CRAN (R 3.5.0)                      |
-|wilson          |   |2.0.0   |2018-06-27 |local (HendrikSchultheis/wilson@NA) |
+|wilson          |   |2.0.0   |2018-06-29 |local (HendrikSchultheis/wilson@NA) |
 
 # Check results
 
diff --git a/revdep/checks.rds b/revdep/checks.rds
index f1e582f2d9de6aa7e14363812d8bb8bb11f68b50..dc78959945e422e14d40f987fe96f00a560a0b90 100644
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diff --git a/revdep/problems.md b/revdep/problems.md
index 0204215..368348c 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -10,7 +10,7 @@
 |language |(EN)                         |
 |collate  |German_Germany.1252          |
 |tz       |Europe/Berlin                |
-|date     |2018-06-27                   |
+|date     |2018-06-29                   |
 
 ## Packages
 
@@ -44,10 +44,8 @@
 |shinycssloaders |   |0.2.0   |2017-05-12 |CRAN (R 3.5.0)                      |
 |shinydashboard  |   |0.7.0   |2018-03-21 |CRAN (R 3.5.0)                      |
 |shinyjs         |   |1.0     |2018-01-08 |CRAN (R 3.5.0)                      |
-|shinythemes     |   |1.1.1   |2016-10-12 |CRAN (R 3.5.0)                      |
 |viridis         |   |0.5.1   |2018-03-29 |CRAN (R 3.5.0)                      |
-|webshot         |   |0.5.0   |2017-11-29 |CRAN (R 3.5.0)                      |
-|wilson          |   |2.0.0   |2018-06-27 |local (HendrikSchultheis/wilson@NA) |
+|wilson          |   |2.0.0   |2018-06-29 |local (HendrikSchultheis/wilson@NA) |
 
 # Check results
 

From f35ee0aeec4a4f21f4ba43556df7458919c12748 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 29 Jun 2018 11:13:22 +0200
Subject: [PATCH 75/75] DESCRIPTION: changed title to title case

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3342e24..74bdc07 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: wilson
 Type: Package
-Title: Web-based Interactive Omics visualizatioN
+Title: Web-Based Interactive Omics Visualization
 Version: 2.0.0
 Authors@R: c(
     person("Hendrik", "Schultheis", email = "hendrik.schultheis@mpi-bn.mpg.de", role = c("aut", "cre")),