annotate 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"

#!/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)