--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FlowSOMGenerateTree.R	Tue Jun 23 12:46:08 2020 -0400
@@ -0,0 +1,250 @@
+#!/usr/bin/Rscript
+# Module for Galaxy
+# Generates FlowSOM reference tree
+# with FlowSOM AggregateFlowFrames
+######################################################################
+#                  Copyright (c) 2017 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Version 1
+# Cristel Thomas
+#
+#
+library(FlowSOM)
+library(flowCore)
+
+generateTree <- function(ff, output="", columns=list(), cluster=10, xgrid=10,
+                         ygrid=10,plot="", plot_pdf=FALSE, mplot="", flag_def=T,
+                         table="", mtable="", flag_meta=FALSE, user_seed=42,
+                         flag_nodesize=F) {
+
+  # check default -- if def get all except FSC/SSC
+  # also check nb of markers/channels and indices
+  markers <- colnames(ff)
+  print_markers <- as.vector(pData(parameters(ff))$desc)
+  # Update print_markers if the $P?S not in the FCS file
+  for (i in 1:length(print_markers)) {
+    if (is.na(print_markers[i])) {
+      print_markers[i] <- markers[i]
+    }
+  }
+
+  if (flag_def){
+    channels_to_exclude <- c(grep(markers, pattern="FSC"),
+                             grep(markers, pattern="SSC"),
+                             grep(markers, pattern="Time"))
+    columns <- markers[-channels_to_exclude]
+  }
+
+  set.seed(user_seed)
+  fs <- ReadInput(ff, compensate=F, transform=F, scale=T)
+  fs <- BuildSOM(fs, colsToUse = columns, xdim=xgrid, ydim=ygrid)
+  fst <- BuildMST(fs, tSNE=T)
+
+  if (!mplot==""){
+    pdf(mplot, useDingbats=FALSE, onefile=TRUE)
+    for (marker in markers){
+      PlotMarker(fst, marker)
+    }
+    dev.off()
+  }
+  metaC <- metaClustering_consensus(fst$map$codes, k=cluster, seed=user_seed)
+
+  if (!plot==""){
+    if (flag_nodesize){
+      fst <- UpdateNodeSize(fst, reset=TRUE)
+      fst$MST$size <- fst$MST$size/2
+    }
+    if (plot_pdf) {
+      pdf(plot, useDingbats=FALSE)
+      PlotStars(fst, backgroundValues = as.factor(metaC))
+      dev.off()
+    } else {
+      png(plot, type="cairo", height=800, width=800)
+      PlotStars(fst, backgroundValues = as.factor(metaC))
+      dev.off()
+    }
+  }
+  if (!table==""){
+    m <- matrix(0,nrow=nrow(ff),ncol=1)
+    s <- seq_len(nrow(ff))
+    if (flag_meta){
+      m[s,] <- metaC[fst$map$mapping[,1]]
+    } else {
+      m[s,] <- fst$map$mapping[,1]
+    }
+    colnames(m) <- "FlowSOM"
+    ff <- cbind2(ff,m)
+    out <- exprs(ff)
+    print_markers <- append(print_markers, "Population")
+    colnames(out) <- print_markers
+    write.table(out, file=table, quote=F, row.names=F, col.names=T, sep='\t',
+                append=F)
+
+    nb_nodes <- max(fst$map$mapping[,1])
+    mm <- matrix(0, nrow=nb_nodes, ncol=2)
+    ss <- seq_len(nb_nodes)
+    mm[,1]<- as.character(ss)
+    mm[ss,2]<- as.character(metaC)
+    colnames(mm) <- c("Node", "Meta-Cluster")
+    write.table(mm, file=mtable, quote=F, row.names=F, col.names=T, sep='\t',
+                append=F)
+
+  }
+  saveRDS(fst, file = output)
+}
+
+flowFrameOrFCS <- function(input, output="", columns=list(),cluster=10,xgrid=10,
+                           ygrid=10,plot="",plot_pdf=FALSE, mplot="", default=T,
+                           table="", mtable="", flag_meta=FALSE, user_seed=42,
+                           nodesize=FALSE) {
+  isValid <- F
+  is_fcs <- F
+  is_ff <- F
+  ff <- ""
+  tryCatch({
+    is_fcs <- isFCSfile(input)
+  }, error = function(ex) {
+    print(paste(ex))
+  })
+
+  if (!is_fcs){
+    tryCatch({
+      ff <- readRDS(input)
+      is_ff <- T
+    }, error = function(ex) {
+      print(paste(ex))
+    })
+  } else {
+    ff <- read.FCS(input, transformation=FALSE)
+  }
+
+  if (!is_ff && !is_fcs) {
+    quit(save = "no", status = 10, runLast = FALSE)
+  } else {
+    for (cols in columns){
+      if (cols > length(colnames(ff))){
+        quit(save = "no", status = 12, runLast = FALSE)
+      }
+    }
+    generateTree(ff, output, columns, cluster, xgrid, ygrid, plot, plot_pdf,
+                 mplot, default, table, mtable, flag_meta, user_seed, nodesize)
+  }
+}
+
+args <- commandArgs(trailingOnly = TRUE)
+flag_default <- FALSE
+columns <- list()
+
+if (args[3] == "" || args[3] == "i.e.:1,2,5") {
+  flag_default <- TRUE
+} else {
+  #rm last X if it's there
+  columns <- as.numeric(strsplit(args[3], ",")[[1]])
+  for (col in columns){
+    if (is.na(col)){
+      quit(save = "no", status = 11, runLast = FALSE)
+    }
+  }
+}
+
+cluster <- 10
+if (!args[4] == ""){
+  if (!is.na(as.integer(args[4]))){
+    cluster <- as.integer(args[4])
+  } else {
+    quit(save = "no", status = 13, runLast = FALSE)
+  }
+}
+
+xgrid <- 10
+if (!args[5] == ""){
+  if (!is.na(as.integer(args[5]))){
+    cluster <- as.integer(args[5])
+  } else {
+    quit(save = "no", status = 14, runLast = FALSE)
+  }
+}
+
+ygrid <- 10
+if (!args[6] == ""){
+  if (!is.na(as.integer(args[6]))){
+    cluster <- as.integer(args[6])
+  } else {
+    quit(save = "no", status = 14, runLast = FALSE)
+  }
+}
+seed <- 42
+if (!args[7]==""){
+  if (!is.na(as.integer(args[7]))){
+    seed <- as.integer(args[7])
+  } else {
+    quit(save = "no", status = 15, runLast = FALSE)
+  }
+}
+
+plot <- ""
+mplot <- ""
+plot_pdf <- FALSE
+table <- ""
+mtable <- ""
+flag_meta <- FALSE
+nodesize <- FALSE
+nb_args <- length(args)
+
+if (nb_args==16) {
+  plot <- args[8]
+  if (args[9]=='PDF') {
+    plot_pdf <- TRUE
+  }
+  nodesize <- args[10]
+  mplot <- args[11]
+  table <- args[13]
+  mtable <- args[14]
+  if (args[12]=='meta'){
+    flag_meta<-TRUE
+  }
+} else if (nb_args==15){
+  plot <- args[8]
+  if (args[9]=='PDF') {
+    plot_pdf <- TRUE
+  }
+  nodesize <- args[10]
+  table <- args[12]
+  mtable <- args[13]
+  if (args[11]=='meta'){
+    flag_meta<-TRUE
+  }
+} else if (nb_args==13) {
+  mplot <- args[8]
+  table <- args[10]
+  mtable <- args[11]
+  if (args[9]=='meta'){
+    flag_meta<-TRUE
+  }
+} else if (nb_args==12) {
+  table <- args[9]
+  mtable <- args[10]
+  if (args[8]=='meta'){
+    flag_meta<-TRUE
+  }
+} else if (nb_args==11) {
+  plot <- args[8]
+  if (args[9]=='PDF') {
+    plot_pdf <- TRUE
+  }
+  nodesize <- args[10]
+  mplot <- args[11]
+} else if (nb_args==10) {
+  plot <- args[8]
+  if (args[9]=='PDF') {
+    plot_pdf <- TRUE
+  }
+  nodesize <- args[10]
+} else if (nb_args==8){
+  mplot <- args[8]
+}
+
+flowFrameOrFCS(args[1], args[2], columns, cluster, xgrid, ygrid, plot, plot_pdf,
+               mplot, flag_default, table, mtable, flag_meta, seed, nodesize)