diff getDensityPlots.R @ 1:413f3e610295 draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getDensityPlots.R	Thu Jul 16 08:00:52 2020 -0400
@@ -0,0 +1,130 @@
+#!/usr/bin/Rscript --vanilla
+# Density Plot Module for Galaxy
+# FlowDensity
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Version 1
+# Cristel Thomas
+#
+#
+
+library(flowCore)
+library(flowDensity)
+
+generateGraph <- function(input, channels, output, plot_default=TRUE,
+                          flag_pdf=FALSE) {
+  fcs <- read.FCS(input, transformation=F)
+  ## marker names
+  markers <- colnames(fcs)
+  print_markers <- as.vector(pData(parameters(fcs))$desc)
+  # Update print_markers if the $P?S not in the FCS file
+  for (i in 1:length(print_markers)) {
+    if (is.na(print_markers[i])) {
+      print_markers[i] <- markers[i]
+    }
+  }
+
+  if (plot_default) {
+    channels <- c(grep(colnames(fcs), pattern="Forward scatter", ignore.case=TRUE),
+                  grep(colnames(fcs), pattern="Side scatter", ignore.case=TRUE))
+    if (length(channels) == 0){
+      channels <- c(grep(colnames(fcs), pattern="FSC"),
+                    grep(colnames(fcs), pattern="SSC"))
+      if (length(channels) > 2) {
+        #get first FSC and corresponding SSC
+        channels <- c(grep(colnames(fcs), pattern="FSC-A"),
+                      grep(colnames(fcs), pattern="SSC-A"))
+        if (length(channels) == 0) {
+          channels <- c(grep(colnames(fcs), pattern="FSC-H"),
+                        grep(colnames(fcs), pattern="SSC-H"))
+          if (length(channels) == 0) {
+            channels <- c(grep(colnames(fcs), pattern="FSC-W"),
+                          grep(colnames(fcs), pattern="SSC-W"))
+          }
+        }
+      }
+    }
+    if (length(channels) == 0) {
+      warning('No forward/side scatter channels found, no plots will be generated.')
+      quit(save = "no", status = 10, runLast = FALSE)
+    }
+  }
+
+  nb_markers <- length(channels)
+  if (nb_markers == 1) {
+    warning('There is only one marker selected to plot.')
+    quit(save = "no", status = 12, runLast = FALSE)
+  }
+  for (j in nb_markers) {
+    if (channels[j] > length(markers)){
+      warning('Please indicate markers between 1 and ', length(markers))
+      quit(save = "no", status = 10, runLast = FALSE)
+    }
+  }
+  nb_rows <- ceiling(((nb_markers-1)*nb_markers)/4)
+  h <- 400 * nb_rows
+  if (flag_pdf) {
+    pdf(output, useDingbats=FALSE, onefile=TRUE)
+    par(mfrow=c(2,2))
+      for (m in 1:(nb_markers - 1)) {
+        for (n in (m+1):nb_markers) {
+          plotDens(fcs, c(channels[m],channels[n]), xlab = print_markers[channels[m]], ylab = print_markers[channels[n]])
+        }
+      }
+    dev.off()
+  } else {
+    png(output, type="cairo", height=h, width=800)
+    par(mfrow=c(nb_rows,2))
+    for (m in 1:(nb_markers - 1)) {
+      for (n in (m+1):nb_markers) {
+        plotDens(fcs, c(channels[m],channels[n]), xlab = print_markers[channels[m]], ylab = print_markers[channels[n]])
+      }
+    }
+    dev.off()
+  }
+}
+
+checkFCS <- function(input_file, channels, output_file, plot_default=TRUE,
+                     flag_pdf=FALSE){
+  isValid <- F
+  # Check file beginning matches FCS standard
+  tryCatch({
+    isValid <- isFCSfile(input_file)
+  }, error = function(ex) {
+    print (paste("    ! Error in isFCSfile", ex))
+  })
+
+  if (isValid) {
+    generateGraph(input_file, channels, output_file, plot_default, flag_pdf)
+  } else {
+    print (paste(input_file, "does not meet FCS standard"))
+  }
+}
+
+args <- commandArgs(trailingOnly = TRUE)
+channels <- list()
+flag_default <- FALSE
+flag_pdf <- FALSE
+
+if (args[2]=="None" || args[2]== "" || args[2] == "i.e.:1,3,4") {
+  flag_default <- TRUE
+} else {
+  channels <- as.numeric(strsplit(args[2], ",")[[1]])
+  for (channel in channels){
+    if (is.na(channel)){
+      quit(save = "no", status = 11, runLast = FALSE)
+    }
+  }
+  if (length(channels) == 1){
+    warning('Please indicate more than one marker to plot.')
+    quit(save = "no", status = 10, runLast = FALSE)
+  }
+}
+
+if (args[4] == "PDF"){
+  flag_pdf <- TRUE
+}
+checkFCS(args[1], channels, args[3], flag_default, flag_pdf)