--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getDensityPlots_text.R	Tue Jul 14 09:40:13 2020 -0400
@@ -0,0 +1,158 @@
+#!/usr/bin/env Rscript
+# Density Plot Module for Galaxy
+# ggplot2
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Version 1
+# Cristel Thomas
+#
+#
+
+library(ggplot2)
+library(grid)
+library(KernSmooth)
+# Multiple plot function
+# from http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_%28ggplot2%29/
+# ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
+# - cols:   Number of columns in layout
+# - layout: A matrix specifying the layout. If present, 'cols' is ignored.
+#
+# If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
+# then plot 1 will go in the upper left, 2 will go in the upper right, and
+# 3 will go all the way across the bottom.
+#
+multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
+  # Make a list from the ... arguments and plotlist
+  plots <- c(list(...), plotlist)
+  numPlots = length(plots)
+
+  # If layout is NULL, then use 'cols' to determine layout
+  if (is.null(layout)) {
+    # Make the panel
+    # ncol: Number of columns of plots
+    # nrow: Number of rows needed, calculated from # of cols
+    layout <- matrix(seq(1, cols * ceiling(numPlots/cols)),
+                    ncol = cols, nrow = ceiling(numPlots/cols))
+  }
+
+ if (numPlots==1) {
+    print(plots[[1]])
+  } else {
+    # Set up the page
+    grid.newpage()
+    pushViewport(viewport(layout = grid.layout(nrow(layout), ncol(layout))))
+
+    # Make each plot, in the correct location
+    for (i in 1:numPlots) {
+      # Get the i,j matrix positions of the regions that contain this subplot
+      matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE))
+      print(plots[[i]], vp = viewport(layout.pos.row = matchidx$row,
+                                      layout.pos.col = matchidx$col))
+    }
+  }
+}
+
+generateGraphFromText <- function(input, channels, output, plot_default=TRUE,
+                                  flag_pdf=FALSE) {
+  fcs <- read.table(input, header = TRUE, sep = "\t", check.names = FALSE)
+  ## marker names
+  markers <- colnames(fcs)
+
+  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)
+  	}
+  }
+
+  plots <- list()
+  i <- 0
+  for (m in 1:(nb_markers - 1)) {
+    for (n in (m+1):nb_markers) {
+      x <- fcs[,channels[m]]
+      y <- fcs[,channels[n]]
+      df <- data.frame(x = x, y = y,
+                       d = densCols(x, y, colramp = colorRampPalette(rev(rainbow(10, end = 4/6)))))
+      p <- ggplot(df) +
+           geom_point(aes(x, y, col = d), size = 0.2) +
+           scale_color_identity() +
+           theme_bw() +
+           labs(x = markers[channels[m]]) +
+           labs(y = markers[channels[n]])
+      i <- i + 1
+      plots[[i]] <- p
+    }
+  }
+  nb_rows <- ceiling(((nb_markers-1)*nb_markers)/4)
+  h <- 400 * nb_rows
+  hp <- 10 * (nb_rows/2)
+
+  if (flag_pdf){
+    pdf(output, height=hp, width=10, useDingbats=FALSE, onefile=TRUE)
+      multiplot(plotlist = plots, cols = 2)
+    dev.off()
+  } else {
+    png(output, type="cairo", width=800, height=h)
+      multiplot(plotlist = plots, cols = 2)
+    dev.off()
+  }
+}
+
+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
+}
+generateGraphFromText(args[1], channels, args[3], flag_default, flag_pdf)