Changed:

- modularized plot download

Added:
- download CSV with cellIDs and cluster assignment
- download CSV after cleaning

global.R

-source('auxfunc.R')
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+source('modules/auxfunc.R')
+source('modules/downPlot.R')
+source('modules/downCellIDsCls.R')
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auxfunc.R → modules/auxfunc.R

@@ -152,8 +152,8 @@ userDataGen <- function() {
   dt.nuc = data.table(Metadata_Site = rep(1:locNsites, each = locNtp * locNtracks),
                       Metadata_Well = rep(1:locNwells, each = locNtp * locNsites * locNtracks / locNwells),
                       Metadata_RealTime = rep(1:locNtp, locNsites* locNtracks),
-                      objCyto_Intensity_MeanIntensity_imErkCor = rnorm(locNtp * locNtracks * locNsites, .5, 0.1),
-                      objNuc_Intensity_MeanIntensity_imErkCor  = rnorm(locNtp * locNtracks * locNsites, .5, 0.1),
+                      objCyto_Intensity_MeanIntensity_imErkCor = c(rnorm(locNtp * locNtracks * locNsites * 0.5, .5, 0.1), rnorm(locNtp * locNtracks * locNsites * 0.5, 1, 0.2)),
+                      objNuc_Intensity_MeanIntensity_imErkCor  = c(rnorm(locNtp * locNtracks * locNsites * 0.5, .25, 0.1), rnorm(locNtp * locNtracks * locNsites * 0.5, .5, 0.2)),
                       TrackLabel = rep(1:(locNtracks*locNsites), each = locNtp))
   
   cat(colnames(dt.nuc))

modules/downCellIDsCls.R

+# RShiny module for downloading cellIDs with cluster numbers
+# Use:
+# in ui.R
+# downPlotUI('uniqueID', "your_label")
+#
+# in server.R
+# callModule(downPlot, "uniqueID", 'fname.pdf', input_plot_to_save)
+
+
+downCellClUI <- function(id, label = "Download Data") {
+  ns <- NS(id)
+  
+  tagList(
+    # Label to display as h4 header
+    h4(label),
+    downloadButton(ns('downCellCl'), 'CSV')
+  )
+}
+
+downCellCl <- function(input, output, session, in.fname, in.data) {
+  
+  output$downCellCl <- downloadHandler(
+    filename = function() {
+      in.fname
+    },
+    
+    content = function(file) {
+      write.csv(x = in.data, file = file, row.names = FALSE)
+    }
+  )
+  
+}
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modules/downPlot.R

+# RShiny module for downloading pdf of the plot
+# Use:
+# in ui.R
+# downPlotUI('uniqueID', "your_label")
+#
+# in server.R
+# callModule(downPlot, "uniqueID", 'fname.pdf', input_plot_to_save)
+
+
+downPlotUI <- function(id, label = "Download Plot") {
+  ns <- NS(id)
+  
+  tagList(
+    # Label to display as h4 header
+    h4(label),
+    
+    fluidRow(
+      column(
+        3,
+        numericInput(
+          ns('inPlotWidth'),
+          "Width",
+          17,
+          min = 1,
+          width = 100
+        )
+      ),
+      column(
+        3,
+        numericInput(
+          ns('inPlotHeight'),
+          "Height",
+          10,
+          min = 1,
+          width = 100
+        )
+      ),
+      column(6,
+             downloadButton(ns('downPlot'), 'PDF'))
+    )
+  )
+}
+
+downPlot <- function(input, output, session, in.fname, in.plot, in.gg = FALSE) {
+
+  output$downPlot <- downloadHandler(
+    filename = function() {
+      in.fname
+    },
+    
+    content = function(file) {
+      if (in.gg) {
+        ggsave(
+          file,
+          limitsize = FALSE,
+          in.plot(),
+          width  = input$inPlotWidth,
+          height = input$inPlotHeight
+        )
+      } else {
+        pdf(file,
+            width  = input$inPlotWidth,
+            height = input$inPlotHeight)
+        
+        in.plot()
+        dev.off()
+      }
+    }
+  )
+  
+}
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