diff FCSflowViz.R @ 0:23c0af6be9a7 draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FCSflowViz.R	Mon Jun 22 20:48:47 2020 -0400
@@ -0,0 +1,128 @@
+#!/usr/bin/Rscript
+# Stacked 1D Density Plot Module for Galaxy
+# flowviz
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Version 1
+# Cristel Thomas
+#
+#
+
+library(flowViz)
+library(methods)
+
+generateStackedPlots <- function(fs, chans=list(), output="", flag_pdf=FALSE) {
+  h <- 800
+  w <- 1200
+  if (length(fs@colnames)>8){
+    h <- 1200
+    w <- 1600
+  }
+  channels_to_plot <- fs@colnames
+  if (length(chans) > 0){
+    channels_to_plot <- fs@colnames[chans]
+  }
+
+  if (flag_pdf) {
+    pdf(output, useDingbats=FALSE, onefile=TRUE)
+    print({
+      densityplot(~., fs, channels = channels_to_plot)
+    })
+    dev.off()
+  } else {
+    png(output, type="cairo", height=h, width=w)
+    print({
+      densityplot(~., fs, channels = channels_to_plot)
+    })
+    dev.off()
+  }
+}
+
+checkFlowSet <- function(fcsfiles, newnames, channels=list(), out_file ="",
+                         flag_pdf=FALSE) {
+
+  isValid <- F
+  markerCheck <- T
+
+  for (i in 1:length(fcsfiles)){
+   is_file_valid <- F
+   tryCatch({
+     fcs <- read.FCS(fcsfiles[i], transformation=FALSE)
+     is_file_valid <- T
+   }, error = function(ex) {
+     print(paste(ex))
+   })
+   if (i == 1) {
+     m1 <- as.vector(pData(parameters(fcs))$desc)
+   } else {
+     m2 <- as.vector(pData(parameters(fcs))$desc)
+     if (is.na(all(m1==m2))) {
+       mm1 <- is.na(m1)
+       mm2 <- is.na(m2)
+       if (all(mm1==mm2)){
+         if (!all(m1==m2, na.rm=TRUE)){
+           markerCheck <- F
+         }
+       } else {
+         markerCheck <- F
+       }
+     } else if (!all(m1==m2)) {
+       markerCheck <- F
+     }
+   }
+  }
+  if (markerCheck) {
+   isValid <- T
+  } else {
+   quit(save = "no", status = 12, runLast = FALSE)
+  }
+
+  if (isValid) {
+    fs <- read.flowSet(files=fcsfiles, transformation=FALSE)
+    fs@phenoData@data$name <- newnames
+    generateStackedPlots(fs, channels, out_file, flag_pdf)
+  } else {
+    quit(save = "no", status = 12, runLast = FALSE)
+  }
+}
+
+args <- commandArgs(trailingOnly = TRUE)
+channels <- list()
+flag_pdf <- FALSE
+
+if (args[1]=="None") {
+  flag_default <- TRUE
+} else {
+  if (args[1] == "i.e.:1,3,4"){
+    flag_default <- TRUE
+  } else {
+    channels <- as.numeric(strsplit(args[1], ",")[[1]])
+    for (channel in channels){
+      if (is.na(channel)){
+        quit(save = "no", status = 11, runLast = FALSE)
+      }
+    }
+  }
+}
+
+if (args[3] == "PDF"){
+  flag_pdf <- TRUE
+}
+
+nb_files <- (length(args) - 3) / 2
+fcsfiles <- character(nb_files)
+newnames <- character(nb_files)
+j <- 1
+## get files and file names
+for (i in 4:length(args)) {
+  if (!i%%2){
+    fcsfiles[[j]] <- args[i]
+    newnames[[j]] <- args[i+1]
+    j <- j + 1
+  }
+}
+
+checkFlowSet(fcsfiles, newnames, channels, args[2], flag_pdf)