Merge branch 'release/v0.1.7'

kircherlab · May 7, 2019 · 045e3d4 · 045e3d4
2 parents 3ab924a + 0d9560f
commit 045e3d4
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Showing 8 changed files with 816 additions and 9 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,34 @@
+dist: trusty   # Use Ubuntu 14.04 image (instead of 12.04)
+language: r
+sudo: false
+r: 3.5.1
+
+# Install packrat if needed and have it restore packages.
+install:
+  - R -e 'if (system.file(package="packrat") == "") install.packages("packrat")'
+  - R -e "packrat::packify(); packrat::restore()"
+
+cache:
+  # Main R library
+  packages: true
+  directories:
+    # Packrat packages
+    - packrat/lib
+    # PhantomJS
+    - travis_phantomjs
+
+# Install PhantomJS (if not cached)
+before_install:
+  - "export PHANTOMJS_VERSION=2.1.1"
+  - "phantomjs --version"
+  - "export PATH=$PWD/travis_phantomjs/phantomjs-$PHANTOMJS_VERSION-linux-x86_64/bin:$PATH"
+  - "hash -r"
+  - "phantomjs --version"
+  - "if [ $(phantomjs --version) != $PHANTOMJS_VERSION ]; then rm -rf $PWD/travis_phantomjs; mkdir -p $PWD/travis_phantomjs; fi"
+  - "if [ $(phantomjs --version) != $PHANTOMJS_VERSION ]; then wget https://github.com/Medium/phantomjs/releases/download/v$PHANTOMJS_VERSION/phantomjs-$PHANTOMJS_VERSION-linux-x86_64.tar.bz2 -O $PWD/travis_phantomjs/phantomjs-$PHANTOMJS_VERSION-linux-x86_64.tar.bz2; fi"
+  - "if [ $(phantomjs --version) != $PHANTOMJS_VERSION ]; then tar -xvf $PWD/travis_phantomjs/phantomjs-$PHANTOMJS_VERSION-linux-x86_64.tar.bz2 -C $PWD/travis_phantomjs; fi"
+  - "if [ $(phantomjs --version) != $PHANTOMJS_VERSION ]; then hash -r; fi"
+  - "phantomjs --version"
+
+script:
+  - R -f run_tests.R
diff --git a/app.R b/app.R
@@ -136,7 +136,8 @@ server <- function(input, output, session) {
                                                    DT::DTOutput(paste0(name,'_table'))
                                   ),
                                  # Plot View using ggplot
-                                 tabPanel("Variant plot", plotlyOutput(paste0(name,'_plot'))
+                                 tabPanel("Variant plot", plotlyOutput(paste0(name,'_plot')),
+                                                          checkboxInput(paste0(name,"_colorblind"), "Colorblind visualization", value = FALSE)
                                  )
                      )
                    )
@@ -151,7 +152,7 @@ server <- function(input, output, session) {
   # function to render the table/plot for a specific selected element (by name)
   # is dependend on the release, barcodes, p-value threshsold, true/false deletions, 
   # range of the plot and needs output and session element
-  renderElement <- function(name,release,barcodes, threshold, deletions, range, output,session) {
+  renderElement <- function(name,release,barcodes, threshold, deletions, range, output,session, colorPalette) {
     # check first if elements are not null
     if(!is.null(release) & !is.null(barcodes) & !is.null(threshold)) {
       # values cannot be NA (possible if out of range is selected, like <1 barcoded)
@@ -178,11 +179,13 @@ server <- function(input, output, session) {
         # and the function getPlot from the same source to plot the ggplot
         plotData <- modify.filterdata(data_general, barcodes,threshold,deletions,range)
         if (plotData %>% nrow > 0) {
+          isolate({
           output[[paste0(name,"_plot")]] <- renderPlotly({
-            p <- getPlot(plotData,name,release)
+            p <- getPlot(plotData,name,release,colorPalette)
             ggplotly(p) %>% 
               layout(autosize=TRUE) %>% layout(xaxis=list(fixedrange=TRUE)) %>% layout(yaxis=list(fixedrange=TRUE)) %>% 
               config(displayModeBar = F)
+          },quoted = TRUE)
           })
         }
       }
@@ -213,15 +216,15 @@ server <- function(input, output, session) {
     isolate({
       appendTab("promoterNavigation", experimentPage(name))
       updateRegionSlider(session, paste0(name,"_region"), name, "GRCh37")
-      renderElement(name,"GRCh37",10,1e-5,TRUE,NULL,output,session)
+      renderElement(name,"GRCh37",10,1e-5,TRUE,NULL,output,session, "default")
     })
   }
   for (name in enhancers$Element){
     session$userData$actualSelectedRelease[[name]] <- "GRCh37"
     isolate({
       appendTab("enhancerNavigation", experimentPage(name))
       updateRegionSlider(session, paste0(name,"_region"), name, "GRCh37")
-      renderElement(name,"GRCh37",10,1e-5,TRUE,NULL,output,session)
+      renderElement(name,"GRCh37",10,1e-5,TRUE,NULL,output,session,"default")
     })
   }
 
@@ -239,8 +242,16 @@ server <- function(input, output, session) {
         release <- input[[paste0(name,"_reference")]]
         barcodes <- input[[paste0(name,"_barcodes")]]
         pValue <- input[[paste0(name,"_pvalue")]]
+
         deletions <- input[[paste0(name,"_deletions")]]
 
+        colorblind <- input[[paste0(name,"_colorblind")]]
+
+        if(!is.null(colorblind) && colorblind) {
+          colorPalette <- "colorblind"
+        } else {
+          colorPalette <- "default"
+        }
 
         # update the slider if the release changed
         if (!is.null(release) && session$userData$actualSelectedRelease[[name]] != release) {
@@ -250,7 +261,7 @@ server <- function(input, output, session) {
         # update data table and plot
         range <- input[[paste0(name,"_region")]]
         isolate({
-          renderElement(name,release,barcodes,pValue,deletions,range,output,session)
+          renderElement(name,release,barcodes,pValue,deletions,range,output,session,colorPalette)
         })
       }
     })