Merge commits from master

.Rbuildignore

@@ -2,3 +2,4 @@
 ^\.Rproj\.user$
 ^\.buildkite.*
 ^revdep$
+^cran-comments.md$

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: wilson
 Type: Package
 Title: Web-Based Interactive Omics Visualization
-Version: 2.0.0
+Version: 2.0.1
 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 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
+Description: Tool-set of modules for creating web-based applications that use plot based strategies to visualize and analyze multi-omics data.
+    This package 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
 Encoding: UTF-8
 LazyData: true
@@ -47,4 +47,9 @@ Imports: shiny,
     methods,
     R6
 RoxygenNote: 6.0.1
-biocViews:
+biocViews: 
+Suggests: knitr,
+    rmarkdown,
+    testthat,
+    vdiffr
+VignetteBuilder: knitr

NEWS.md

@@ -0,0 +1,25 @@
+# wilson 2.0.1
+- tests added
+# wilson 2.0.0 
+## Features
+- clarion class:
+  - easier data-format validation by providing several checks
+  - simplified module usage (only forward clarion object) for top-level modules (e.g. filter & plot)
+  - provide functions for frequent tasks (e.g. get_name, is_delimited, etc.)
+
+- geneView: 
+  - group columns by one or more factors
+
+- pca:
+  - color & shape grouping by selected factor(s)
+
+- scatterPlot:
+  - add name to hovertext if available (only interactive)
+
+## Misc
+- improved notifications (closable, more)
+- overall code quality improvements via usage of packages goodpractice and lintr
+- removed deprecated colorPicker
+
+# wilson 1.0.0
+first public release

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, color = NULL), n = 200, contour = FALSE)
 
     plot <- plot + ggplot2::scale_fill_gradient(low = "white", high = "black") +
       # guides(fill=FALSE) +		# remove density legend
@@ -1152,7 +1152,7 @@ searchData <- function(input, choices, options = c("=", "<", ">"), min. = min(ch
       }
 
       # range
-      if ("inner" == options){
+      if ("inner" == options) {
         if (x >= input[1] & x <= input[2]) return(TRUE)
       }
       if ("outer" == options) {
@@ -1203,15 +1203,17 @@ searchData <- function(input, choices, options = c("=", "<", ">"), min. = min(ch
 download <- function(file, filename, plot, width, height, ppi = 72, save_plot = TRUE, ui = NULL) {
   session <- shiny::getDefaultReactiveDomain()
 
-  # show notification
-  shiny::showNotification(
-    id = session$ns("download-note"),
-    shiny::tags$b("Preparing download files. Please wait..."),
-    duration = NULL,
-    closeButton = FALSE,
-    type = "message"
-  )
-  shinyjs::runjs(paste0("$(document.getElementById('", paste0("shiny-notification-", session$ns("download-note")), "')).addClass('notification-position-center');"))
+  if (!is.null(session)) {
+    # show notification
+    shiny::showNotification(
+      id = session$ns("download-note"),
+      shiny::tags$b("Preparing download files. Please wait..."),
+      duration = NULL,
+      closeButton = FALSE,
+      type = "message"
+    )
+    shinyjs::runjs(paste0("$(document.getElementById('", paste0("shiny-notification-", session$ns("download-note")), "')).addClass('notification-position-center');"))
+  }
 
   # cut off file extension
   name <- sub("(.*)\\..*$", replacement = "\\1", filename)
@@ -1283,8 +1285,10 @@ download <- function(file, filename, plot, width, height, ppi = 72, save_plot =
   # remove tmp files
   file.remove(files)
 
-  # remove notification
-  shiny::removeNotification(session$ns("download-note"))
+  if (!is.null(session)) {
+    # remove notification
+    shiny::removeNotification(session$ns("download-note"))
+  }
 
   return(out)
 }

R/global.R

@@ -11,8 +11,10 @@ wilson.globals <- new.env(parent = emptyenv())
 #'
 #' @export
 set_logger <- function(logger, token = NULL) {
-  if (is.null(logger) || methods::is(logger, "logger")) {
+  if (methods::is(logger, "logger")) {
     assign(x = paste0("logger", token), value = logger, envir = wilson.globals)
+  } else if (is.null(logger)) {
+    rm(list = paste0("logger", token), envir = wilson.globals)
   }
 }
 

R/parser.R

@@ -25,6 +25,8 @@
 #' @param version pre-header information about version (optional)
 #' @param experiment_id pre-header information about experiment id (optional)
 #'
+#' @return TRUE on success
+#'
 #' @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)) {
@@ -85,7 +87,7 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
   # @return String level of given column
   get_sample_level <- function(col_head, isSample, full_list) {
     # Get the level of all 'sample' columns.
-    # Default: level <- "sample"
+    # Default: level is "sample"
     if (grepl("Ratio", col_head, perl = TRUE)) {
       if (grepl("type", col_head, perl = TRUE)) return("feature")
       return("contrast")
@@ -165,7 +167,7 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
   # @param version version number
   # @param exp_id experiment id
   # @param pGroups data table protein groups file
-  write_clarion_file <- function(meta, out, format, version, exp_id, pGroups, delimiter){
+  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)
@@ -188,10 +190,21 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
   # reading files in data tables
   proteinGroups <- data.table::fread(proteinGroups_in, header = TRUE, quote = "")
   summary_file <- data.table::fread(summary_in, header = TRUE)
-  meta_config <- rjson::fromJSON(file = config)
+
+  meta_config <- tryCatch({
+    rjson::fromJSON(file = config)
+  }, error = function(cond) {
+    stop("Could not read config file")
+  }, warning = function(w) {
+    stop("Could not read config file")
+  })
 
   # getting experiment names
-  exp_names <- (unique(summary_file[Experiment != "", Experiment]))
+  if ("Experiment" %in% colnames(summary_file)) {
+    exp_names <- unique(summary_file[Experiment != "", Experiment])
+  } else {
+    stop("wrong format on summary file: column \'Experiment\' misssing")
+  }
 
   meta <- get_meta_from_config(meta_config = meta_config)
 
@@ -203,6 +216,9 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
   sample_ary <- meta_config$type_array
   reduced_list <- meta_config$reduced_list
   full_sample_list <- c(sample_scores, sample_ratios, sample_probability, sample_category, sample_ary)
+  if (is.null(reduced_list)) {
+    stop("reduced_list is missing in config file")
+  }
 
   # get column names
   col_names <- colnames(proteinGroups)
@@ -214,7 +230,7 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
   # append rows to data table with metadata
   samples_list <- lapply(col_names, function(col_head) {
 
-    unlist(lapply(exp_names, function(name){
+    unlist(lapply(exp_names, function(name) {
       name_brackets <- paste0("\\Q", name)
       exp_regex <- paste0("\\Q ", name)
       sample_description <- strsplit(col_head, exp_regex)
@@ -286,6 +302,8 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce
   # 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)
+
+  return(TRUE)
 }
 
 #' Method to parse input file.

R/release_questions.R

@@ -0,0 +1,8 @@
+#' Defines additional questions asked before CRAN submission.
+#' DO NOT EXPORT!
+release_questions <- function() {
+  c(
+    "Re-run reverse dependencies?",
+    "Abide good practices?"
+  )
+}

README.md

@@ -1,5 +1,5 @@
 # WIlsON: Webbased Interactive Omics visualizatioN -  The R Package
-*Buildkite:* [![Build status](https://badge.buildkite.com/d79f55bb3e3cf0d70d6784feb8c6e26182d602f534e74fac4e.svg?branch=master)](https://buildkite.com/loosolab/wilson)
+*Buildkite:* ![Build status](https://badge.buildkite.com/d79f55bb3e3cf0d70d6784feb8c6e26182d602f534e74fac4e.svg?branch=master)
 
 ## Abstract
 #### Objective
@@ -12,9 +12,9 @@ The WIlsON R package employs the R Shiny and Plotly web-based frameworks using a
 The WIlsON R package includes a toolbox of R Shiny modules that can be used to construct a wide array of web-interfaces for plotting feature-based data.
 
 ## Availability
-All components of the WIlsON R package have been implemented in an integrated web application that is available for download from the Github repository [wilson-apps](https://github.molgen.mpg.de/loosolab/wilson-apps) and can be tested on our [official demonstration server](http://loosolab.mpi-bn.mpg.de/apps/wilson/).
+All components of the WIlsON R package have been implemented in an integrated web application that is available for download from the Github repository [wilson-apps](https://github.molgen.mpg.de/loosolab/wilson-apps/) and can be tested on our [official demonstration server](http://loosolab.mpi-bn.mpg.de/apps/wilson/).
 
-Usage instructions can be found in the extensive [documentation](https://github.molgen.mpg.de/loosolab/wilson-apps/wiki).
+Usage instructions can be found in the extensive [documentation](https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/).
 
 Get a Docker container [here](https://hub.docker.com/r/loosolab/wilson/).
 
@@ -37,7 +37,7 @@ CLARION: generiC fiLe formAt foR quantItative cOmparsions of high throughput scr
 
 CLARION is a data format especially developed to be used with WIlsON, which relies on a tab-delimited table with a metadata header to describe the following columns. It is based on the Summarized Experiment format and supports all types of data which can be reduced to features and their annotation (e.g. genes, transcripts, proteins, probes) with assigned numerical values (e.g. count, score, log2foldchange, z-score, p-value). Most result tables derived from RNA-Seq, ChIP/ATAC-Seq, Proteomics, Microarrays, and many other analyses can thus be easily reformatted to become compatible without having to modify the code of WIlsON for each specific experiment.
 
-Please check the following link for details considering the [CLARION format](https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format).
+Please check the following link for details considering the [CLARION format](https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format/).
 
 ## How to cite
 *Schultheis H, Kuenne C, Preussner J, Wiegandt R, Fust A, Bentsen M, Looso M*. WIlsON: Webbased Interactive Omics VisualizatioN. (2018), doi: https://XY

cran-comments.md

@@ -0,0 +1,57 @@
+# Submission 1
+## Test environments
+* local windows 7 install, R 3.5.1
+* debian 9.4, R 3.4.1
+* win-builder (devel and release)
+
+## R CMD check results
+There were no ERRORs or WARNINGs.
+
+There was 1 NOTE:
+
+* New submission
+
+* Possibly mis-spelled words in DESCRIPTION:
+  Omics (3:30)
+  omics (9:126)
+
+  Both are spelled correctly. First is capital because of title case.
+
+## Downstream dependencies
+I have also run R CMD check on downstream dependencies of wilson 
+(https://github.molgen.mpg.de/loosolab/wilson/tree/master/revdep). 
+All packages that I could install passed.
+
+## Reviewer comments
+Thanks, we see you have lots of cuntions without examples (which may be reasonable given they are not intended t be called by users directly). 
+Nevertheless, it would be good to have them tested, so please create, if examples are not feasible, at least tests that execute the various functions in your package.
+
+Best,
+Uwe Ligges
+
+# Submission 2
+## Test environments
+* local windows 7 install, R 3.5.1
+* debian 9.4, R 3.4.1
+* win-builder (devel and release)
+
+## Submission comments
+Addressed reviewer comments by adding tests where possible.
+
+## R CMD check results
+There were no ERRORs or WARNINGs.
+
+There was 1 NOTE:
+
+* New submission
+
+* Possibly mis-spelled words in DESCRIPTION:
+  Omics (3:30)
+  omics (9:126)
+
+  Both are spelled correctly. First is capital because of title case.
+
+## Downstream dependencies
+I have also run R CMD check on downstream dependencies of wilson 
+(https://github.molgen.mpg.de/loosolab/wilson/tree/master/revdep). 
+All packages that I could install passed.