From 1c117fea7ec5ce990534f1a939de33dd508c1b71 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 10 Jan 2018 11:04:31 +0100
Subject: [PATCH 01/25] create_heatmap: param scale added (only working with
 static)

---
 R/function.R | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/R/function.R b/R/function.R
index 0296f9f..9cc1de7 100644
--- a/R/function.R
+++ b/R/function.R
@@ -405,11 +405,12 @@ create_pca <- function(data, dimensionA = 1, dimensionB = 2, dimensions = 6, on.
 #' @param width Set width of plot in cm (Default = "auto").
 #' @param height Set height of plot in cm (Default = "auto").
 #' @param ppi Pixel per inch (default = 72).
+#' @param scale Modify plot size while preserving aspect ratio (Default = 1).
 #'
 #' @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) {
+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) {
   requireNamespace("heatmaply", quietly = TRUE)
   requireNamespace("ComplexHeatmap", quietly = TRUE)
   requireNamespace("grDevices", quietly = TRUE)
@@ -570,9 +571,9 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
       column_dend_height = grid::unit(1, "inches"),
       row_names_max_width = grid::unit(8, "inches"),
       column_names_max_height = grid::unit(4, "inches"),
-      row_names_gp = grid::gpar(fontsize = 12),
-      column_names_gp = grid::gpar(fontsize = 12),
-      column_title_gp = grid::gpar(fontsize = 10, units = "in"),
+      row_names_gp = grid::gpar(fontsize = 12 * scale),
+      column_names_gp = grid::gpar(fontsize = 12 * scale),
+      column_title_gp = grid::gpar(fontsize = 10 * scale, units = "in"),
       heatmap_legend_param = list(
         color_bar = "continuous",
         legend_direction = "horizontal"
@@ -580,10 +581,10 @@ 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
+    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){
@@ -631,7 +632,7 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
       height <- 500
     }
 
-    plot <- list(plot = plot, width = width, height = height, ppi = ppi, exceed_size = exceed_size)
+    plot <- list(plot = plot, width = width * scale, height = height * scale, ppi = ppi, exceed_size = exceed_size)
   }
 
   return(plot)

From 67b2b75db4a8c4b025a9187b623434809b59210a Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 10 Jan 2018 11:18:37 +0100
Subject: [PATCH 02/25] create_heatmap: static -> scale legend fonts aswell

---
 R/function.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/function.R b/R/function.R
index 9cc1de7..c03adb6 100644
--- a/R/function.R
+++ b/R/function.R
@@ -576,7 +576,9 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
       column_title_gp = grid::gpar(fontsize = 10 * scale, units = "in"),
       heatmap_legend_param = list(
         color_bar = "continuous",
-        legend_direction = "horizontal"
+        legend_direction = "horizontal",
+        title_gp = grid::gpar(fontsize = 10 * scale),
+        labels_gp = grid::gpar(fontsize = 8 * scale)
       )
     )
 

From 8819a8f9e7bca7db936edf3fc9475e928641c4ea Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 10 Jan 2018 11:39:56 +0100
Subject: [PATCH 03/25] create_heatmap: scale legend

---
 R/function.R | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/R/function.R b/R/function.R
index c03adb6..412aac1 100644
--- a/R/function.R
+++ b/R/function.R
@@ -567,10 +567,10 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
       show_column_names = column.label,
       row_names_side = "left",
       row_dend_side = "right",
-      row_dend_width = grid::unit(1, "inches"),
-      column_dend_height = grid::unit(1, "inches"),
-      row_names_max_width = grid::unit(8, "inches"),
-      column_names_max_height = grid::unit(4, "inches"),
+      row_dend_width = grid::unit(1 * scale, "inches"),
+      column_dend_height = grid::unit(1 * scale, "inches"),
+      row_names_max_width = grid::unit(8 * scale, "inches"),
+      column_names_max_height = grid::unit(4 * scale, "inches"),
       row_names_gp = grid::gpar(fontsize = 12 * scale),
       column_names_gp = grid::gpar(fontsize = 12 * scale),
       column_title_gp = grid::gpar(fontsize = 10 * scale, units = "in"),
@@ -578,7 +578,8 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
         color_bar = "continuous",
         legend_direction = "horizontal",
         title_gp = grid::gpar(fontsize = 10 * scale),
-        labels_gp = grid::gpar(fontsize = 8 * scale)
+        labels_gp = grid::gpar(fontsize = 8 * scale),
+        grid_height = grid::unit(0.15 * scale, "inches")
       )
     )
 

From bc05d6cbb6bbcb0b02bdcd8672e971f067edeedb Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 10 Jan 2018 14:56:10 +0100
Subject: [PATCH 04/25] create_heatmap: complexHeatmap row_dend_gp (not
 operational)

---
 R/function.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/function.R b/R/function.R
index 412aac1..3fb529c 100644
--- a/R/function.R
+++ b/R/function.R
@@ -568,7 +568,9 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
       row_names_side = "left",
       row_dend_side = "right",
       row_dend_width = grid::unit(1 * scale, "inches"),
+      # row_dend_gp = grid::gpar(lwd = 1, lex = scale), # don't seem to work
       column_dend_height = grid::unit(1 * scale, "inches"),
+      # column_dend_gp = grid::gpar(lwd = 1, lex = scale), # don't seem to work
       row_names_max_width = grid::unit(8 * scale, "inches"),
       column_names_max_height = grid::unit(4 * scale, "inches"),
       row_names_gp = grid::gpar(fontsize = 12 * scale),

From d2a8a22555a4ba5a85201c022957a176ff9b6fa5 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 10 Jan 2018 14:57:13 +0100
Subject: [PATCH 05/25] global_cor_heatmap: param scale added

---
 R/global_cor_heatmap.R | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/R/global_cor_heatmap.R b/R/global_cor_heatmap.R
index 4ea4aea..8aada9a 100644
--- a/R/global_cor_heatmap.R
+++ b/R/global_cor_heatmap.R
@@ -157,13 +157,14 @@ global_cor_heatmapUI <- function(id) {
 #' @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) {
+global_cor_heatmap <- function(input, output, session, data, types, plot.method = "static", width = "auto", height = "auto", ppi = 72, scale = 1) {
   # load module -------------------------------------------------------------
   # handle reactive data
   data_r <- shiny::reactive({
@@ -180,6 +181,7 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
     width <- ifelse(shiny::is.reactive(width), width(), width)
     height <- ifelse(shiny::is.reactive(height), height(), height)
     ppi <- ifelse(shiny::is.reactive(ppi), ppi(), ppi)
+    scale <- ifelse(shiny::is.reactive(scale), scale(), scale)
 
     if(!is.numeric(width) || width <= 0) {
       width <- "auto"
@@ -197,7 +199,8 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
 
     list(width = width,
          height = height,
-         ppi = ppi)
+         ppi = ppi,
+         scale = scale)
   })
 
   # load internal modules
@@ -346,7 +349,8 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
       height = size()$height,
       ppi = size()$ppi,
       plot.method = plot.method,
-      winsorize.colors = colorPicker()$winsorize
+      winsorize.colors = colorPicker()$winsorize,
+      scale = size()$scale
     )
 
     # update progress indicator

From fbb0c00fe9dab9583111d3f70dc3962e552271d6 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 10 Jan 2018 14:58:55 +0100
Subject: [PATCH 06/25] global_cor_heatmap_example: scaleing slider

---
 exec/global_cor_heatmap_example.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/exec/global_cor_heatmap_example.R b/exec/global_cor_heatmap_example.R
index 361273b..01d31f5 100644
--- a/exec/global_cor_heatmap_example.R
+++ b/exec/global_cor_heatmap_example.R
@@ -17,7 +17,8 @@ ui <- dashboardPage(
   header = dashboardHeader(),
   sidebar = dashboardSidebar(
     numericInput(inputId = "width", label = "width in cm", value = 0, min = 0),
-    numericInput(inputId = "height", label = "height in cm", value = 0, min = 0)
+    numericInput(inputId = "height", label = "height in cm", value = 0, min = 0),
+    sliderInput(inputId = "scale", label = "scale plot", value = 1, min = 1, max = 10)
   ),
   dashboardBody(
     fluidPage(
@@ -27,7 +28,7 @@ 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))
+  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))
 
   shiny::observe({
     print(table())

From df3abcbc2168424e83793bdfb8196c924ac58c48 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Wed, 10 Jan 2018 14:59:34 +0100
Subject: [PATCH 07/25] manuals added

---
 man/create_heatmap.Rd     | 4 +++-
 man/global_cor_heatmap.Rd | 5 ++++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/man/create_heatmap.Rd b/man/create_heatmap.Rd
index e626291..c425135 100644
--- a/man/create_heatmap.Rd
+++ b/man/create_heatmap.Rd
@@ -8,7 +8,7 @@ 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)
+  width = "auto", height = "auto", ppi = 72, scale = 1)
 }
 \arguments{
 \item{data}{data.table containing plot data. First column contains row labels.}
@@ -40,6 +40,8 @@ create_heatmap(data, unitlabel = "auto", row.label = T,
 \item{height}{Set height of plot in cm (Default = "auto").}
 
 \item{ppi}{Pixel per inch (default = 72).}
+
+\item{scale}{Modify plot size while preserving aspect ratio (Default = 1).}
 }
 \value{
 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.
diff --git a/man/global_cor_heatmap.Rd b/man/global_cor_heatmap.Rd
index 8f3a512..80e86b8 100644
--- a/man/global_cor_heatmap.Rd
+++ b/man/global_cor_heatmap.Rd
@@ -5,7 +5,8 @@
 \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)
+  plot.method = "static", width = "auto", height = "auto", ppi = 72,
+  scale = 1)
 }
 \arguments{
 \item{input}{Shiny's input object}
@@ -29,6 +30,8 @@ column4 = sub_label (optional, added to id/ label)}
 \item{height}{Height of the plot in cm. Defaults to minimal size for readable labels and supports reactive.}
 
 \item{ppi}{Pixel per inch. Defaults to 72 and supports reactive.}
+
+\item{scale}{Scale plot size. Defaults to 1, supports reactive.}
 }
 \value{
 Reactive containing data used for plotting.

From 8ede3c83862ed2aedbd984ede82c4fdf269d89c6 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 09:28:34 +0100
Subject: [PATCH 08/25] create_heatmap: now working scale with interactive
 plots

---
 R/function.R | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/R/function.R b/R/function.R
index 3fb529c..3dc0e8d 100644
--- a/R/function.R
+++ b/R/function.R
@@ -459,7 +459,7 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
                                 hclust_method = clustmethod,
                                 dist_method = clustdist,
                                 dendrogram = clustering,
-                                distfun = factoextra::get_dist
+                                distfun = factoextra::get_dist,
                                 #width = width, #not working
                                 #height = height
     )
@@ -482,6 +482,10 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
       height <- auto_height
     }
 
+    # add scale
+    width <- width * scale
+    height <- height * scale
+
     # size exceeded?
     exceed_size <- FALSE
     limit <- 500 * (ppi / 2.54)

From 04dbf0b9508446f8db399aebdf223c919ef42c42 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 09:36:47 +0100
Subject: [PATCH 09/25] heatmap: support plot scaleing

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

diff --git a/R/heatmap.R b/R/heatmap.R
index c21cf92..a6a7e2c 100644
--- a/R/heatmap.R
+++ b/R/heatmap.R
@@ -103,11 +103,12 @@ heatmapUI <- function(id, row.label = TRUE) {
 #' @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
-heatmap <- function(input, output, session, data, types, plot.method = "static", custom.row.label = NULL, label.sep = ", ", width = "auto", height = "auto", ppi = 72) {
+heatmap <- function(input, output, session, data, types, plot.method = "static", custom.row.label = NULL, label.sep = ", ", width = "auto", height = "auto", ppi = 72, scale = 1) {
   # cluster limitation
   static <- 11000
   interactive <- 3000
@@ -125,6 +126,7 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
     width <- ifelse(shiny::is.reactive(width), width(), width)
     height <- ifelse(shiny::is.reactive(height), height(), height)
     ppi <- ifelse(shiny::is.reactive(ppi), ppi(), ppi)
+    scale <- ifelse(shiny::is.reactive(scale), scale(), scale)
 
     if(!is.numeric(width) || width <= 0) {
       width <- "auto"
@@ -142,7 +144,8 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
 
     list(width = width,
          height = height,
-         ppi = ppi)
+         ppi = ppi,
+         scale = scale)
   })
 
   # Fetch the reactive guide for this module
@@ -277,6 +280,7 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
       width = size()$width,
       height = size()$height,
       ppi = size()$ppi,
+      scale = size()$scale,
       plot.method = plot.method,
       winsorize.colors = colorPicker()$winsorize
     )
diff --git a/man/heatmap.Rd b/man/heatmap.Rd
index cd9bd68..077dbf4 100644
--- a/man/heatmap.Rd
+++ b/man/heatmap.Rd
@@ -6,7 +6,7 @@
 \usage{
 heatmap(input, output, session, data, types, plot.method = "static",
   custom.row.label = NULL, label.sep = ", ", width = "auto",
-  height = "auto", ppi = 72)
+  height = "auto", ppi = 72, scale = 1)
 }
 \arguments{
 \item{input}{Shiny's input object}
@@ -34,6 +34,8 @@ column4: sub_label (optional, added to id/ label)}
 \item{height}{Height of the plot in cm. Defaults to minimal size for readable labels and supports reactive.}
 
 \item{ppi}{Pixel per inch. Defaults to 72 and supports reactive.}
+
+\item{scale}{Scale plot size. Defaults to 1, supports reactive.}
 }
 \value{
 Reactive containing data used for plotting.

From 7976c0e0fa00308ae4981e7e7d2a43407598d462 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 09:37:46 +0100
Subject: [PATCH 10/25] heatmap_example: use scaleing

---
 exec/heatmap_example.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/exec/heatmap_example.R b/exec/heatmap_example.R
index 53e083b..771c75e 100644
--- a/exec/heatmap_example.R
+++ b/exec/heatmap_example.R
@@ -18,7 +18,8 @@ names(metadata)[1] <- "key"
 
 ui <- dashboardPage(header = dashboardHeader(), sidebar = dashboardSidebar(
   numericInput(inputId = "width", label = "width in cm", value = 0, min = 0),
-  numericInput(inputId = "height", label = "height in cm", value = 0, min = 0)
+  numericInput(inputId = "height", label = "height in cm", value = 0, min = 0),
+  sliderInput(inputId = "scale", label = "scale plot", value = 1, min = 1, max = 10)
 ), dashboardBody(fluidPage(
   heatmapUI("id")
 )))
@@ -32,7 +33,7 @@ server <- function(input, output) {
     metadata[ type != "annotation"]
   })
 
-  heat <- callModule(heatmap, "id", data = table, types = typ, plot.method = "static", custom.row.label = table, width = reactive(input$width), height = reactive(input$height))
+  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))
 
   observe({
     print(heat())

From c7ed1cae20cc57d441001aa91399f2106445ade4 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 12:55:09 +0100
Subject: [PATCH 11/25] create_heatmap: scale texts aswell (interactive);
 create_geneView: implemented scaleing

---
 R/function.R           | 21 +++++++++++++++------
 man/create_geneview.Rd |  4 +++-
 2 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/R/function.R b/R/function.R
index 3dc0e8d..4b5bd13 100644
--- a/R/function.R
+++ b/R/function.R
@@ -442,7 +442,7 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
   if(plot.method == "interactive"){
     #estimate label sizes
     #row label
-    rowlabel_size <- ifelse(row.label, max(nchar(data[[1]]), na.rm = TRUE) * 8, 0)
+    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
@@ -459,7 +459,7 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
                                 hclust_method = clustmethod,
                                 dist_method = clustdist,
                                 dendrogram = clustering,
-                                distfun = factoextra::get_dist,
+                                distfun = factoextra::get_dist
                                 #width = width, #not working
                                 #height = height
     )
@@ -467,10 +467,14 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
     #layout
     plot <- heatmaply::heatmaply(plot,
                                  plot_method = "ggplot",
-                                 scale_fill_gradient_fun = ggplot2::scale_fill_gradientn(colors = colors, name = unitlabel, limits = winsorize.colors, oob = scales::squish)
+                                 scale_fill_gradient_fun = ggplot2::scale_fill_gradientn(colors = colors, name = unitlabel, limits = winsorize.colors, oob = scales::squish),
+                                 heatmap_layers = ggplot2::theme(text = ggplot2::element_text(size = 12 * scale))
     )
 
-    plot <- plotly::layout(plot, autosize = ifelse(width == "auto", TRUE, FALSE), margin = list(l = rowlabel_size, r = legend, b = collabel_size))
+    # scale axis ticks
+    ticks <- list(tickfont = list(size = 12 * scale))
+
+    plot <- plotly::layout(plot, autosize = ifelse(width == "auto", TRUE, FALSE), margin = list(l = rowlabel_size, r = legend, b = collabel_size), xaxis = ticks, yaxis2 = ticks)
 
     # decide which sizes should be used
     if(width == "auto") {
@@ -664,13 +668,14 @@ create_heatmap <- function(data, unitlabel='auto', row.label=T, row.custom.label
 #' @param width Set the width of the plot in cm (default = "auto").
 #' @param height Set the height of the plot in cm (default = "auto").
 #' @param ppi Pixel per inch (default = 72).
+#' @param scale Modify plot size while preserving aspect ratio (Default = 1).
 #'
 #' @details Width/ height limit = 500. If exceeded default to 500 and issue exceed_size = TRUE.
 #'
 #' @import data.table
 #'
 #' @return Returns depending on plot.method list(plot = ggplot/ plotly object, width = width in cm, height = height in cm, ppi = pixel per inch, exceed_size = Boolean).
-create_geneview <- function(data, grouping, plot.type = "line", facet.target = "gene", facet.cols = 2, colors = NULL, ylabel = NULL, ylimits = NULL, gene.label = NULL, plot.method = "static", width = "auto", height = "auto", ppi = 72){
+create_geneview <- function(data, grouping, plot.type = "line", facet.target = "gene", facet.cols = 2, colors = NULL, ylabel = NULL, ylimits = NULL, gene.label = NULL, plot.method = "static", width = "auto", height = "auto", ppi = 72, scale = 1){
   #grouping
   #group by factor if existing (fill with key if empty)
   grouping[grouping[[2]] == "", 2 := grouping[grouping[[2]] == "", 1]]
@@ -773,7 +778,7 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
       legend.position = "none",														#remove legend
       legend.title = ggplot2::element_blank(),
       axis.title.x = ggplot2::element_blank(),
-      text = ggplot2::element_text(family = "mono", size = 15)
+      text = ggplot2::element_text(family = "mono", size = 15 * scale)
 
       #axis.line.x = element_line(size = .3),
       #axis.line.y = element_line(size = .3),
@@ -967,6 +972,10 @@ create_geneview <- function(data, grouping, plot.type = "line", facet.target = "
     height <- auto_height
   }
 
+  # add scaleing factor
+  width <- width * scale
+  height <- height * scale
+
   # size exceeded?
   exceed_size <- FALSE
   if(width > 500) {
diff --git a/man/create_geneview.Rd b/man/create_geneview.Rd
index 7117b8a..8ca3d08 100644
--- a/man/create_geneview.Rd
+++ b/man/create_geneview.Rd
@@ -7,7 +7,7 @@
 create_geneview(data, grouping, plot.type = "line", facet.target = "gene",
   facet.cols = 2, colors = NULL, ylabel = NULL, ylimits = NULL,
   gene.label = NULL, plot.method = "static", width = "auto",
-  height = "auto", ppi = 72)
+  height = "auto", ppi = 72, scale = 1)
 }
 \arguments{
 \item{data}{data.table containing plot data}
@@ -37,6 +37,8 @@ column2 : factor1}
 \item{height}{Set the height of the plot in cm (default = "auto").}
 
 \item{ppi}{Pixel per inch (default = 72).}
+
+\item{scale}{Modify plot size while preserving aspect ratio (Default = 1).}
 }
 \value{
 Returns depending on plot.method list(plot = ggplot/ plotly object, width = width in cm, height = height in cm, ppi = pixel per inch, exceed_size = Boolean).

From 88a85debfc21ccc8c2575e0a5510a74669d889c3 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 12:57:12 +0100
Subject: [PATCH 12/25] geneView: param scale added

---
 R/geneView.R    | 10 +++++++---
 man/geneView.Rd |  4 +++-
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/R/geneView.R b/R/geneView.R
index 7ce41c8..773c15a 100644
--- a/R/geneView.R
+++ b/R/geneView.R
@@ -98,6 +98,7 @@ geneViewUI <- function(id, plot.columns = 3){
 #' @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.
 #'
 #' @details Width/ height/ ppi less or equal to default will use default value.
 #' @details Ppi less or equal to zero will use default.
@@ -106,7 +107,7 @@ geneViewUI <- function(id, plot.columns = 3){
 #'
 #' @export
 
-geneView <- function(input, output, session, data, metadata, level = NULL, plot.method = "static", custom.label = NULL, label.sep = ", ", width = "auto", height = "auto", ppi = 72){
+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)){
@@ -136,6 +137,7 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
     width <- ifelse(shiny::is.reactive(width), width(), width)
     height <- ifelse(shiny::is.reactive(height), height(), height)
     ppi <- ifelse(shiny::is.reactive(ppi), ppi(), ppi)
+    scale <- ifelse(shiny::is.reactive(scale), scale(), scale)
 
     if(!is.numeric(width) || width <= 0) {
       width <- "auto"
@@ -149,7 +151,8 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
 
     list(width = width,
          height = height,
-         ppi = ppi)
+         ppi = ppi,
+         scale = scale)
   })
 
   #Fetch the reactive guide for this module
@@ -279,7 +282,8 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
       plot.method = plot.method,
       width = size()$width,
       height = size()$height,
-      ppi = size()$ppi
+      ppi = size()$ppi,
+      scale = size()$scale
     )
 
     progress$set(1, detail = "Return plot")
diff --git a/man/geneView.Rd b/man/geneView.Rd
index b33b235..b8e755d 100644
--- a/man/geneView.Rd
+++ b/man/geneView.Rd
@@ -6,7 +6,7 @@
 \usage{
 geneView(input, output, session, data, metadata, level = NULL,
   plot.method = "static", custom.label = NULL, label.sep = ", ",
-  width = "auto", height = "auto", ppi = 72)
+  width = "auto", height = "auto", ppi = 72, scale = 1)
 }
 \arguments{
 \item{input}{Shiny's input object.}
@@ -38,6 +38,8 @@ column3: level (condition type)}
 \item{height}{Height of the plot in cm. Defaults to minimal size for readable labels and supports reactive.}
 
 \item{ppi}{Pixel per inch. Defaults to 72 and supports reactive.}
+
+\item{scale}{Scale plot size. Defaults to 1, supports reactive.}
 }
 \value{
 Reactive containing data.table used for plotting.

From c62ab61a5eb68e580cdf7e3873478f03c8beffef Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 12:57:34 +0100
Subject: [PATCH 13/25] geneView_example: scale added

---
 exec/geneView_example.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/exec/geneView_example.R b/exec/geneView_example.R
index bddb915..4441db5 100644
--- a/exec/geneView_example.R
+++ b/exec/geneView_example.R
@@ -18,7 +18,8 @@ names(metadata)[1] <- "key"
 
 ui <- dashboardPage(header = dashboardHeader(), sidebar = dashboardSidebar(
   numericInput(inputId = "width", label = "width in cm", value = 0, min = 0),
-  numericInput(inputId = "height", label = "height in cm", value = 0, min = 0)
+  numericInput(inputId = "height", label = "height in cm", value = 0, min = 0),
+  sliderInput(inputId = "scale", label = "scale plot", value = 1, min = 1, max = 10)
 ), dashboardBody(fluidPage(
   geneViewUI("id")
 )))
@@ -34,7 +35,7 @@ server <- function(input, output) {
     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))
+  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))
 
   observe({
     print(gene())

From fce6c61fd88e752ddeef4828ad79470f1ea8fa29 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 13:11:22 +0100
Subject: [PATCH 14/25] create_pca: added param scale

---
 R/function.R      | 19 ++++++++++++-------
 man/create_pca.Rd |  5 ++++-
 2 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/R/function.R b/R/function.R
index 4b5bd13..d63be2d 100644
--- a/R/function.R
+++ b/R/function.R
@@ -281,6 +281,7 @@ create_scatterplot <- function(data, transparency = 1, pointsize = 1, labelsize
 #' @param width Set the width of the plot in cm (default = 28).
 #' @param height Set the height of the plot in cm (default = 28).
 #' @param ppi Pixel per inch (default = 72).
+#' @param scale Modify plot size while preserving aspect ratio (Default = 1).
 #'
 #' @details If width and height are the same axis ratio will be set to one (quadratic plot).
 #' @details Width/ height limit = 500. If exceeded default to 500 and issue exceed_size = TRUE.
@@ -288,7 +289,7 @@ create_scatterplot <- function(data, transparency = 1, pointsize = 1, labelsize
 #' @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) {
+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) {
   requireNamespace("FactoMineR", quietly = TRUE)
   requireNamespace("factoextra", quietly = TRUE)
 
@@ -345,16 +346,16 @@ create_pca <- function(data, dimensionA = 1, dimensionB = 2, dimensions = 6, on.
     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),
-    axis.title.y = ggplot2::element_text(color="black", size=11),
+    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)						#size for all (legend?) labels
+    legend.title = ggplot2::element_blank(),
+    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, label = "none", axes.linetype = "blank", repel = FALSE)
+  pca_plot <- factoextra::fviz_pca_ind(pca, axes = c(dimensionA, dimensionB), invisible = "none", pointsize = pointsize * scale, label = "none", axes.linetype = "blank", repel = FALSE)
   pca_plot <- pca_plot + theme1
 
   if(labels) {
@@ -362,7 +363,7 @@ create_pca <- function(data, dimensionA = 1, dimensionB = 2, dimensions = 6, on.
       data = data.frame(pca$ind$coord),
       mapping = ggplot2::aes_(x = pca$ind$coord[, dimensionA], y = pca$ind$coord[, dimensionB], label = rownames(pca$ind$coord)),
       segment.color = "gray65",
-      size = labelsize,
+      size = labelsize * scale,
       force = 2,
       max.iter = 10000,
       point.padding = grid::unit(0.1, "lines")
@@ -374,6 +375,10 @@ create_pca <- function(data, dimensionA = 1, dimensionB = 2, dimensions = 6, on.
   #   pca_plot <- pca_plot + ggplot2::coord_fixed(ratio = 1)
   # }
 
+  # add scale factor
+  width <- width * scale
+  height <- height * scale
+
   # size exceeded?
   exceed_size <- FALSE
   if(width > 500) {
diff --git a/man/create_pca.Rd b/man/create_pca.Rd
index 044613d..fbb0e70 100644
--- a/man/create_pca.Rd
+++ b/man/create_pca.Rd
@@ -6,7 +6,8 @@
 \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)
+  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).}
@@ -32,6 +33,8 @@ create_pca(data, dimensionA = 1, dimensionB = 2, dimensions = 6,
 \item{height}{Set the height of the plot in cm (default = 28).}
 
 \item{ppi}{Pixel per inch (default = 72).}
+
+\item{scale}{Modify plot size while preserving aspect ratio (Default = 1).}
 }
 \value{
 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).

From 6452b225c3025e154ff82a19676686caff8d937a Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 13:12:30 +0100
Subject: [PATCH 15/25] pca: added parameter scale

---
 R/pca.R    | 10 +++++++---
 man/pca.Rd |  4 +++-
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/R/pca.R b/R/pca.R
index b50a544..7b07791 100644
--- a/R/pca.R
+++ b/R/pca.R
@@ -77,6 +77,7 @@ pcaUI <- function(id, show.label = TRUE) {
 #' @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.
+#' @param scale Scale plot size. Defaults to 1, supports reactive.
 #'
 #' @details Width/ height/ ppi less or equal to zero will use default value.
 #'
@@ -85,7 +86,7 @@ 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) {
+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)){
@@ -124,6 +125,7 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
     width <- ifelse(shiny::is.reactive(width), width(), width)
     height <- ifelse(shiny::is.reactive(height), height(), height)
     ppi <- ifelse(shiny::is.reactive(ppi), ppi(), ppi)
+    scale <- ifelse(shiny::is.reactive(scale), scale(), scale)
 
     if(!is.numeric(width) | width <= 0) {
       width <- 28
@@ -137,7 +139,8 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
 
     list(width = width,
          height = height,
-         ppi = ppi)
+         ppi = ppi,
+         scale = scale)
   })
 
 
@@ -248,7 +251,8 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
                on.columns = TRUE,
                width = size()$width,
                height = size()$height,
-               ppi = size()$ppi
+               ppi = size()$ppi,
+               scale = size()$scale
     )
 
     progress$set(1)
diff --git a/man/pca.Rd b/man/pca.Rd
index c6f509e..eee0778 100644
--- a/man/pca.Rd
+++ b/man/pca.Rd
@@ -5,7 +5,7 @@
 \title{pca module server logic}
 \usage{
 pca(input, output, session, data, types, levels = NULL, entryLabel = NULL,
-  width = 28, height = 28, ppi = 72)
+  width = 28, height = 28, ppi = 72, scale = 1)
 }
 \arguments{
 \item{input}{Shiny's input object}
@@ -31,6 +31,8 @@ column4: sub_label (optional, added to id/ label)}
 \item{height}{Height of the plot in cm. Defaults to 28 and supports reactive.}
 
 \item{ppi}{Pixel per inch. Defaults to 72 and supports reactive.}
+
+\item{scale}{Scale plot size. Defaults to 1, supports reactive.}
 }
 \value{
 A reactive containing list with dimensions.

From e2bfbc965d770f8a04f0075d4080b85abe490502 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 13:13:38 +0100
Subject: [PATCH 16/25] pca_example: scale slider added

---
 exec/pca_example.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/exec/pca_example.R b/exec/pca_example.R
index 7cc78af..d7be244 100644
--- a/exec/pca_example.R
+++ b/exec/pca_example.R
@@ -14,13 +14,14 @@ names(metadata)[1] <- "key"
 
 ui <- dashboardPage(header = dashboardHeader(), sidebar = dashboardSidebar(
   numericInput(inputId = "width", label = "width in cm", value = 0, min = 0),
-  numericInput(inputId = "height", label = "height in cm", value = 0, min = 0)
+  numericInput(inputId = "height", label = "height in cm", value = 0, min = 0),
+  sliderInput(inputId = "scale", label = "scale plot", min = 1, max = 10, value = 1)
 ), dashboardBody(fluidPage(
   pcaUI("id")
 )))
 
 server <- function(input, output) {
-  callModule(pca, "id", data = data, types = metadata, levels = metadata[level != "annotation"][["level"]], width = reactive(input$width), height = reactive(input$height))
+  callModule(pca, "id", data = data, types = metadata, levels = metadata[level != "annotation"][["level"]], width = reactive(input$width), height = reactive(input$height), scale = reactive(input$scale))
 }
 
 # Run the application

From 912d8f22e1d28cc78a80579622d80ce412e04752 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 13:35:39 +0100
Subject: [PATCH 17/25] create_scatterplot: add param scale

---
 R/function.R              | 42 ++++++++++++++++++++++-----------------
 man/create_scatterplot.Rd |  4 +++-
 2 files changed, 27 insertions(+), 19 deletions(-)

diff --git a/R/function.R b/R/function.R
index d63be2d..dc4dfa5 100644
--- a/R/function.R
+++ b/R/function.R
@@ -23,13 +23,14 @@
 #' @param height Set plot height in cm (Default = "auto").
 #' @param ppi Pixel per inch (default = 72).
 #' @param plot.method Whether the plot should be 'interactive' or 'static' (Default = 'static').
+#' @param scale Modify plot size while preserving aspect ratio (Default = 1).
 #'
 #' @details Width/ height limit = 500. If exceeded default to 500 and issue exceed_size = TRUE.
 #'
 #' @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"){
+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){
   ########## prepare data ##########
   #set labelnames if needed
   x_label <- ifelse(nchar(x_label), x_label, names(data)[2])
@@ -50,10 +51,10 @@ create_scatterplot <- function(data, transparency = 1, pointsize = 1, labelsize
   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)))
+  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])))
+    rows.to.keep.high <- which(as.logical((highlight.data[, 2] != 0) + (highlight.data[, 3 != 0])))
     highlight.data <- highlight.data[rows.to.keep.high]
   }
 
@@ -71,11 +72,12 @@ create_scatterplot <- function(data, transparency = 1, pointsize = 1, labelsize
     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(face="bold", color="black", size=10),
-    axis.title.y = ggplot2::element_text(face="bold", color="black", size=10),
-    plot.title = ggplot2::element_text(face="bold", 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(face = "bold", color = "black", size = 10 * scale),
+    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!
   )
@@ -148,7 +150,7 @@ create_scatterplot <- function(data, transparency = 1, pointsize = 1, labelsize
     }
 
     #set points
-    plot <- plot + ggplot2::geom_point(size=pointsize, alpha=transparency, ggplot2::aes(text = hovertext))
+    plot <- plot + ggplot2::geom_point(size = pointsize * scale, alpha = transparency, ggplot2::aes(text = hovertext))
 
     if(!is.null(highlight.data)){
       #set highlighted hovertext
@@ -164,27 +166,27 @@ create_scatterplot <- function(data, transparency = 1, pointsize = 1, labelsize
       }
 
       #set highlighted points
-      plot <- plot + ggplot2::geom_point(size = pointsize, 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 = hovertext.high))
     }
   # static points without hovertexts
   } else if(plot.method == "static") {
     seed <- Sys.getpid() + Sys.time()
     # set points
-    plot <- plot + ggplot2::geom_point(size = pointsize, alpha = transparency)
+    plot <- plot + ggplot2::geom_point(size = pointsize * scale, alpha = transparency)
 
     # set highlighted points
     if(!is.null(highlight.data)) {
-      plot <- plot + ggplot2::geom_point(size = pointsize, alpha = transparency, inherit.aes = TRUE, data = highlight.data, color = highlight.color, show.legend = FALSE)
+      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)) {
-        plot <- plot + ggrepel::geom_label_repel(data = highlight.data, mapping = ggplot2::aes(label = highlight.labels), size = labelsize, color = "black", segment.color = "gray65", force = 2, max.iter = 10000, 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, color = "black", segment.color = "gray65", force = 2, max.iter = 10000, point.padding = grid::unit(0.1, "lines"), label.size = NA, fill = NA, 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 = 10000, 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 = 10000, 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, color = "black", segment.color = "gray65", force = 2, max.iter = 10000, 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, color = "black", segment.color = "gray65", force = 2, max.iter = 10000, point.padding = grid::unit(0.1, "lines"), label.size = NA, fill = NA, 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 = 10000, 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 = 10000, point.padding = grid::unit(0.1, "lines"), label.size = NA, fill = NA, seed = seed)
     }
   }
 
@@ -234,6 +236,10 @@ create_scatterplot <- function(data, transparency = 1, pointsize = 1, labelsize
     height <- height * (ppi / 2.54)
   }
 
+  # apply scale factor
+  width <- width * scale
+  height <- height * scale
+
   # size exceeded?
   exceed_size <- FALSE
   limit <- 500 * (ppi / 2.54)
@@ -252,9 +258,9 @@ create_scatterplot <- function(data, transparency = 1, pointsize = 1, labelsize
     # 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, font = list(size = labelsize), 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)')
       } 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, font = list(size = labelsize), bgcolor = 'rgba(255, 255, 255, 0.5)')
+        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)')
       }
     }
   }
diff --git a/man/create_scatterplot.Rd b/man/create_scatterplot.Rd
index 8c3985d..1eb26de 100644
--- a/man/create_scatterplot.Rd
+++ b/man/create_scatterplot.Rd
@@ -9,7 +9,7 @@ create_scatterplot(data, transparency = 1, pointsize = 1, labelsize = 3,
   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")
+  ppi = 72, plot.method = "static", scale = 1)
 }
 \arguments{
 \item{data}{data.table containing plot data
@@ -55,6 +55,8 @@ column 2, 3(, 4): x, y(, z)}
 \item{ppi}{Pixel per inch (default = 72).}
 
 \item{plot.method}{Whether the plot should be 'interactive' or 'static' (Default = 'static').}
+
+\item{scale}{Modify plot size while preserving aspect ratio (Default = 1).}
 }
 \value{
 Returns list(plot = ggplotly/ ggplot, width, height, ppi, exceed_size).

From 75110769ded7ed64943a9630089ca80efe76dba8 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 13:35:54 +0100
Subject: [PATCH 18/25] scatterPlot: scale param added

---
 R/scatterPlot.R    | 10 +++++++---
 man/scatterPlot.Rd |  4 +++-
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/R/scatterPlot.R b/R/scatterPlot.R
index 1fc2a8b..f79229b 100644
--- a/R/scatterPlot.R
+++ b/R/scatterPlot.R
@@ -122,13 +122,14 @@ scatterPlotUI <- function(id) {
 #' @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 Returns reactive containing data used for plot.
 #'
 #' @details Make sure to have the same columnnames in data and features.
 #'
 #' @export
-scatterPlot <- function(input, output, session, data, types, features = NULL, markerReac = NULL, plot.method = "static", width = "auto", height = "auto", ppi = 72) {
+scatterPlot <- function(input, output, session, data, types, 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)){
@@ -154,6 +155,7 @@ scatterPlot <- function(input, output, session, data, types, features = NULL, ma
     width <- ifelse(shiny::is.reactive(width), width(), width)
     height <- ifelse(shiny::is.reactive(height), height(), height)
     ppi <- ifelse(shiny::is.reactive(ppi), ppi(), ppi)
+    scale <- ifelse(shiny::is.reactive(scale), scale(), scale)
 
     if(!is.numeric(width) || width <= 0) {
       width <- "auto"
@@ -167,7 +169,8 @@ scatterPlot <- function(input, output, session, data, types, features = NULL, ma
 
     list(width = width,
          height = height,
-         ppi = ppi)
+         ppi = ppi,
+         scale = scale)
   })
 
   #Fetch the reactive guide for this module
@@ -333,7 +336,8 @@ scatterPlot <- function(input, output, session, data, types, features = NULL, ma
       plot.method = plot.method,
       width = size()$width,
       height = size()$height,
-      ppi = size()$ppi
+      ppi = size()$ppi,
+      scale = size()$scale
     )
 
     progress$set(1)
diff --git a/man/scatterPlot.Rd b/man/scatterPlot.Rd
index c7e94e6..53dc5c2 100644
--- a/man/scatterPlot.Rd
+++ b/man/scatterPlot.Rd
@@ -6,7 +6,7 @@
 \usage{
 scatterPlot(input, output, session, data, types, features = NULL,
   markerReac = NULL, plot.method = "static", width = "auto",
-  height = "auto", ppi = 72)
+  height = "auto", ppi = 72, scale = 1)
 }
 \arguments{
 \item{input}{Shiny's input object}
@@ -34,6 +34,8 @@ column4: sub_label (optional, added to id/ label)}
 \item{height}{Height of the plot in cm. Defaults to minimal size for readable labels and supports reactive.}
 
 \item{ppi}{Pixel per inch. Defaults to 72 and supports reactive.}
+
+\item{scale}{Scale plot size. Defaults to 1, supports reactive.}
 }
 \value{
 Returns reactive containing data used for plot.

From 5ae409a6f7fda74401c4a6c26f952756b99a4bbe Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 13:36:19 +0100
Subject: [PATCH 19/25] scatterPlot_example: scale slider added

---
 exec/scatterPlot_example.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/exec/scatterPlot_example.R b/exec/scatterPlot_example.R
index d65489c..2728010 100644
--- a/exec/scatterPlot_example.R
+++ b/exec/scatterPlot_example.R
@@ -20,7 +20,8 @@ ui <- dashboardPage(header = dashboardHeader(),
                     sidebar = dashboardSidebar(
                       markerUI("marker"),
                       numericInput(inputId = "width", label = "width in cm", value = 0, min = 0),
-                      numericInput(inputId = "height", label = "height in cm", value = 0, min = 0)
+                      numericInput(inputId = "height", label = "height in cm", value = 0, min = 0),
+                      sliderInput(inputId = "scale", label = "scale plot", min = 1, max = 10, value = 1)
                     ),
                     body = dashboardBody(
                       fluidPage(
@@ -32,7 +33,7 @@ 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[level != "annotation"], features = data[am == 1], markerReac = marker, plot.method = "static", width = reactive(input$width), height = reactive(input$height))
+  plot <- callModule(scatterPlot, "id", data = data, types = metadata[level != "annotation"], features = data[am == 1], markerReac = marker, plot.method = "interactive", width = reactive(input$width), height = reactive(input$height), scale = reactive(input$scale))
 
   observe({
     print(plot())

From 35cf2c1138231163ce5f86c45d5e1674ed2cef8a Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 14:30:23 +0100
Subject: [PATCH 20/25] pca: clear plot on reset

---
 R/pca.R | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/R/pca.R b/R/pca.R
index 7b07791..53de734 100644
--- a/R/pca.R
+++ b/R/pca.R
@@ -149,6 +149,9 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
     rintrojs::introjs(session, options = list(steps = guide()))
   })
 
+  # clear plot
+  clearPlot <- shiny::reactiveVal(value = FALSE)
+
   #reset ui
   shiny::observeEvent(input$reset, {
     shinyjs::reset("label")
@@ -157,6 +160,7 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
     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")
+    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")
@@ -233,6 +237,7 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
   computed.data <- shiny::eventReactive(input$plot, {
     # enable downloadButton
     shinyjs::enable("download")
+    clearPlot(FALSE)
 
     #new progress indicator
     progress <- shiny::Progress$new()
@@ -257,6 +262,9 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
 
     progress$set(1)
 
+    # show plot
+    shinyjs::show("pca")
+
     return(plot)
   })
 
@@ -276,7 +284,11 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel =
     width = plot_width,
     height = plot_height,
     {
-      computed.data()$plot
+      if(clearPlot()){
+        return()
+      } else {
+        computed.data()$plot
+      }
     })
 
   #group data by dimension

From b8bbba519a84581452308c63ead77f6374854643 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 14:38:19 +0100
Subject: [PATCH 21/25] geneView: clear plot on reset

---
 R/geneView.R | 46 ++++++++++++++++++++++++++++++----------------
 1 file changed, 30 insertions(+), 16 deletions(-)

diff --git a/R/geneView.R b/R/geneView.R
index 773c15a..251497d 100644
--- a/R/geneView.R
+++ b/R/geneView.R
@@ -161,6 +161,10 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
     rintrojs::introjs(session, options = list(steps = guide()))
   })
 
+  # clear plot
+  clearPlot <- shiny::reactiveVal(FALSE)
+
+  # reset
   shiny::observeEvent(input$reset, {
     shinyjs::reset("genes")
     shinyjs::reset("plotType")
@@ -173,6 +177,7 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
       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({
@@ -255,6 +260,7 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
   plot <- shiny::eventReactive(input$plot, {
     # enable downloadButton
     shinyjs::enable("download")
+    clearPlot(FALSE)
 
     #new progress indicator
     progress <- shiny::Progress$new()
@@ -328,30 +334,38 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot.
 
   if(plot.method == "interactive") {
     output$interactive <- plotly::renderPlotly({
-      #progress indicator
-      progress <- shiny::Progress$new()
-      on.exit(progress$close())
-      progress$set(message = "Rendering plot", value = 0)
-
-      plot <- plot()$plot
-
-      progress$set(value = 1)
-      return(plot)
-    })
-  } else if(plot.method == "static") {
-    output$static <- shiny::renderPlot(
-      width = shiny::reactive(plot()$width * (plot()$ppi / 2.54)),
-      height = shiny::reactive(plot()$height * (plot()$ppi / 2.54)),
-      {
+      if(clearPlot()) {
+        return()
+      } else {
         #progress indicator
         progress <- shiny::Progress$new()
         on.exit(progress$close())
-        progress$set(message = "Rendering plot", value = 0.3)
+        progress$set(message = "Rendering plot", value = 0)
 
         plot <- plot()$plot
 
         progress$set(value = 1)
         return(plot)
+      }
+    })
+  } else if(plot.method == "static") {
+    output$static <- shiny::renderPlot(
+      width = shiny::reactive(plot()$width * (plot()$ppi / 2.54)),
+      height = shiny::reactive(plot()$height * (plot()$ppi / 2.54)),
+      {
+        if(clearPlot()) {
+          return()
+        } else {
+          #progress indicator
+          progress <- shiny::Progress$new()
+          on.exit(progress$close())
+          progress$set(message = "Rendering plot", value = 0.3)
+
+          plot <- plot()$plot
+
+          progress$set(value = 1)
+          return(plot)
+        }
       })
   }
 

From 4d8fe8beb43b3614c74078034e773899041b4c34 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 14:43:07 +0100
Subject: [PATCH 22/25] limit: fixed bug where ui wasn't reset

---
 R/limit.R | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/R/limit.R b/R/limit.R
index 9b3e436..e7499f7 100644
--- a/R/limit.R
+++ b/R/limit.R
@@ -28,6 +28,11 @@ limitUI <- function(id, label = "Limit"){
 #'
 #' @export
 limit <- function(input, output, session, lower = NULL, upper = NULL){
+  # reset on re-run
+  shinyjs::reset("enable")
+  shinyjs::reset("lowerLimit")
+  shinyjs::reset("upperLimit")
+
   # evaluate reactive parameter
   lower.r <- shiny::reactive({
     if(shiny::is.reactive(lower)) {

From 9f71cb83d8e2bd1491fef51fe8a9de8246de3dca Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 15:12:12 +0100
Subject: [PATCH 23/25] scatterPlot: hide plot on reset; fixed limit reset bug

---
 R/scatterPlot.R | 38 +++++++++++++++++++++++++-------------
 1 file changed, 25 insertions(+), 13 deletions(-)

diff --git a/R/scatterPlot.R b/R/scatterPlot.R
index f79229b..71b0f59 100644
--- a/R/scatterPlot.R
+++ b/R/scatterPlot.R
@@ -182,6 +182,9 @@ scatterPlot <- function(input, output, session, data, types, features = NULL, ma
   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$reset, {
     shinyjs::reset("density")
@@ -194,8 +197,9 @@ scatterPlot <- function(input, output, session, data, types, features = NULL, ma
     colorPicker <<- shiny::callModule(colorPicker2, "color", distribution = list("sequential", "diverging"), winsorize = winsorize)
     transform_x <<- shiny::callModule(transformation, "transform_x", data = data_x)
     transform_y <<- shiny::callModule(transformation, "transform_y", data = data_y)
-    limit_x <<- shiny::callModule(limit, "xaxis_limit", lower = shiny::reactive(get_x_limit()[1]), upper = shiny::reactive(get_x_limit()[2]))
-    limit_y <<- shiny::callModule(limit, "yaxis_limit", lower = shiny::reactive(get_y_limit()[1]), upper = shiny::reactive(get_y_limit()[2]))
+    limit_x <<- shiny::callModule(limit, "xaxis_limit", lower = shiny::reactive(result.data()$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]))
+    clearPlot(TRUE)
   })
 
   winsorize <- shiny::reactive({
@@ -297,6 +301,7 @@ scatterPlot <- function(input, output, session, data, types, features = NULL, ma
   plot <- shiny::eventReactive(input$plot, {
     #enable downloadbutton
     shinyjs::enable("download")
+    clearPlot(FALSE)
 
     #new progress indicator
     progress <- shiny::Progress$new()
@@ -362,22 +367,29 @@ scatterPlot <- function(input, output, session, data, types, features = NULL, ma
       width = shiny::reactive(plot()$width * (plot()$ppi / 2.54)),
       height = shiny::reactive(plot()$height * (plot()$ppi / 2.54)),
       {
-        plot()$plot
+        if(clearPlot()) {
+          return()
+        } else {
+          plot()$plot
+        }
       }
     )
   } else if(plot.method == "interactive") {
     output$interactive <- plotly::renderPlotly({
-      #new progress indicator
-      progress <- shiny::Progress$new()
-      on.exit(progress$close())
-      progress$set(0.2, message = "Render plot")
-
-      plot <- plot()$plot
-
-      progress$set(1)
-      return(plot)
+      if(clearPlot()) {
+        return()
+      } else {
+        #new progress indicator
+        progress <- shiny::Progress$new()
+        on.exit(progress$close())
+        progress$set(0.2, message = "Render plot")
+
+        plot <- plot()$plot
+
+        progress$set(1)
+        return(plot)
+      }
     })
-
   }
 
   output$download <- shiny::downloadHandler(filename = "scatterPlot.zip",

From 3a81ef2a5e946faa35c761b4cf2d907c84e33e45 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 15:24:45 +0100
Subject: [PATCH 24/25] heatmap: clear plot on reset

---
 R/heatmap.R | 43 ++++++++++++++++++++++++++++---------------
 1 file changed, 28 insertions(+), 15 deletions(-)

diff --git a/R/heatmap.R b/R/heatmap.R
index a6a7e2c..df9c9ec 100644
--- a/R/heatmap.R
+++ b/R/heatmap.R
@@ -208,7 +208,10 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
     }
   })
 
-  #reset ui
+  # clear plot
+  clearPlot <- shiny::reactiveVal(FALSE)
+
+  # reset ui
   shiny::observeEvent(input$reset, {
     shinyjs::reset("cluster.distance")
     shinyjs::reset("cluster.method")
@@ -223,6 +226,7 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
     if(!is.null(custom.row.label)) {
       custom_label <<- shiny::callModule(label, "labeller", data = custom.row.label, label = "Select row label", sep = label.sep, disable = shiny::reactive(!input$row.label))
     }
+    clearPlot(TRUE)
   })
 
   columns <- shiny::callModule(columnSelector, "select", type.columns = types, columnTypeLabel = "Column types to choose from")
@@ -252,6 +256,7 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
   plot <- shiny::eventReactive(input$plot, {
     # enable downloadButton
     shinyjs::enable("download")
+    clearPlot(FALSE)
 
     #new progress indicator
     progress <- shiny::Progress$new()
@@ -296,16 +301,20 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
     })
 
     output$interactive <- plotly::renderPlotly({
-      #new progress indicator
-      progress <- shiny::Progress$new()
-      on.exit(progress$close())
-      progress$set(0.2, message = "Render plot")
+      if(clearPlot()) {
+        return()
+      } else {
+        #new progress indicator
+        progress <- shiny::Progress$new()
+        on.exit(progress$close())
+        progress$set(0.2, message = "Render plot")
 
-      plot <- plot()$plot
+        plot <- plot()$plot
 
-      progress$set(1)
+        progress$set(1)
 
-      return(plot)
+        return(plot)
+      }
     })
   }else{
     output$heatmap <- shiny::renderUI({
@@ -316,15 +325,19 @@ heatmap <- function(input, output, session, data, types, plot.method = "static",
       width = shiny::reactive(plot()$width * (plot()$ppi / 2.54)),
       height = shiny::reactive(plot()$height * (plot()$ppi / 2.54)),
       {
-        #new progress indicator
-        progress <- shiny::Progress$new()
-        on.exit(progress$close())
-        progress$set(0.2, message = "Render plot")
+        if(clearPlot()) {
+          return()
+        } else {
+          #new progress indicator
+          progress <- shiny::Progress$new()
+          on.exit(progress$close())
+          progress$set(0.2, message = "Render plot")
 
-        plot <- plot()$plot
+          plot <- plot()$plot
 
-        progress$set(1)
-        return(ComplexHeatmap::draw(plot, heatmap_legend_side = "bottom"))
+          progress$set(1)
+          return(ComplexHeatmap::draw(plot, heatmap_legend_side = "bottom"))
+        }
     })
   }
 

From c8da6c4be7e73a252530e25f7fdbc17e7c9b510b Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 12 Jan 2018 15:29:52 +0100
Subject: [PATCH 25/25] global_cor_heatmap: clear plot on reset

---
 R/global_cor_heatmap.R | 48 +++++++++++++++++++++++++++---------------
 1 file changed, 31 insertions(+), 17 deletions(-)

diff --git a/R/global_cor_heatmap.R b/R/global_cor_heatmap.R
index 8aada9a..4ffd71b 100644
--- a/R/global_cor_heatmap.R
+++ b/R/global_cor_heatmap.R
@@ -220,6 +220,9 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
   }
 
   # functionality -----------------------------------------------------------
+  # clear plot
+  clearPlot <- shiny::reactiveVal(FALSE)
+
   # reset ui
   shiny::observeEvent(input$reset, {
     shinyjs::reset("calc")
@@ -233,6 +236,7 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
     columns <<- shiny::callModule(columnSelector, "select", type.columns = types, columnTypeLabel = "Column types to choose from")
     transform <<- shiny::callModule(transformation, "transform", data = shiny::reactive(as.matrix(data_r()[, columns$selectedColumns(), with = FALSE])))
     colorPicker <<- shiny::callModule(colorPicker2, "color", distribution = shiny::reactive(tolower(input$distribution)), winsorize = shiny::reactive(equalize(result_data()[, -1])))
+    clearPlot(TRUE)
   })
 
   # warning if plot size exceeds limits
@@ -311,6 +315,8 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
   plot <- shiny::eventReactive(input$plot, {
     # enable downloadButton
     shinyjs::enable("download")
+    # show plot
+    clearPlot(FALSE)
 
     # progress indicator
     progress <- shiny::Progress$new()
@@ -365,34 +371,42 @@ global_cor_heatmap <- function(input, output, session, data, types, plot.method
       width = shiny::reactive(plot()$width * (plot()$ppi / 2.54)),
       height = shiny::reactive(plot()$height * (plot()$ppi / 2.54)),
       {
+        if(clearPlot()) {
+          return()
+        } else {
+          # progress indicator
+          progress <- shiny::Progress$new()
+          on.exit(progress$close())
+          progress$set(0.2, message = "Rendering plot")
+
+          # get plot
+          plot <- plot()$plot
+
+          # update progress indicator
+          progress$set(1)
+
+          # draw plot
+          return(ComplexHeatmap::draw(plot, heatmap_legend_side = "bottom"))
+        }
+      }
+    )
+  }else if(plot.method == "interactive") {
+    output$interactive <- plotly::renderPlotly({
+      if(clearPlot()) {
+        return()
+      } else {
         # progress indicator
         progress <- shiny::Progress$new()
         on.exit(progress$close())
         progress$set(0.2, message = "Rendering plot")
 
-        # get plot
         plot <- plot()$plot
 
         # update progress indicator
         progress$set(1)
 
-        # draw plot
-        return(ComplexHeatmap::draw(plot, heatmap_legend_side = "bottom"))
+        return(plot)
       }
-    )
-  }else if(plot.method == "interactive") {
-    output$interactive <- plotly::renderPlotly({
-      # progress indicator
-      progress <- shiny::Progress$new()
-      on.exit(progress$close())
-      progress$set(0.2, message = "Rendering plot")
-
-      plot <- plot()$plot
-
-      # update progress indicator
-      progress$set(1)
-
-      return(plot)
     })
   }