--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/editFCSmarkers.R	Mon Jun 22 20:07:30 2020 -0400
@@ -0,0 +1,131 @@
+#!/usr/bin/Rscript
+# modify channels and marker names in FCS
+#
+######################################################################
+#                  Copyright (c) 2017 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Cristel Thomas
+# Version 2 - May 2018
+# Modified to take in marker/channel names by name rather than index
+#
+library(flowCore)
+
+checkCandM <- function(m_set, channels=vector(), markers=vector()){
+  if (m_set[[3]]){
+    in_file <- m_set[[1]] %in% channels
+  } else {
+    in_file <- m_set[[1]] %in% markers
+  }
+  if (sum(in_file)==0) {
+    warning("Given original columns are either not in the channels or in the markers of the read object. Will fail.")
+    return(FALSE)
+  }
+  return(TRUE)
+}
+
+modifyMarkersFCS <- function(input, output="", report="", flag_fcs=F,
+                             marker_sets=list()) {
+
+  fcs <- read.FCS(input, transformation=F)
+  original_channels <- colnames(fcs)
+  original_markers <- as.vector(pData(parameters(fcs))$desc)
+  nb <- length(original_channels)
+  ## check if markers are in FCS files
+  check_markers <- sapply(marker_sets, checkCandM, channels=original_channels,
+                          markers=original_markers)
+  if (sum(check_markers)==0) {
+    quit(save = "no", status = 13, runLast = FALSE)
+  }
+
+  post_channels <- colnames(fcs)
+  post_markers <- as.vector(pData(parameters(fcs))$desc)
+
+  for (m_set in marker_sets) {
+    if (m_set[[3]]){
+      chan_to_replace <- post_channels %in% m_set[[1]]
+      for (i in 1:nb){
+        if (chan_to_replace[[i]]){
+          post_channels[[i]] <- m_set[[2]][[match(post_channels[[i]], m_set[[1]])[1]]]
+        }
+      }
+    } else {
+      marker_to_replace <- post_markers %in% m_set[[1]]
+      for (i in 1:nb){
+        if (marker_to_replace[[i]]){
+          post_markers[[i]] <- m_set[[2]][[match(post_markers[[i]], m_set[[1]])[1]]]
+          pm <- paste("$P", as.character(i), "S", sep="")
+          fcs@description[[pm]] <- post_markers[[i]]
+        }
+      }
+    }
+  }
+
+  colnames(fcs) <- post_channels
+  pData(parameters(fcs))$desc <- post_markers
+
+  # write report
+  sink(report)
+  cat("###########################\n")
+  cat("##    BEFORE RENAMING    ##\n")
+  cat("###########################\nFCS Channels\n")
+  cat("---------------------------\n")
+  cat(original_channels,"---------------------------", "FCS Markers","---------------------------",original_markers, sep="\n")
+  cat("\n###########################\n")
+  cat("##    AFTER  RENAMING    ##\n")
+  cat("###########################\nFCS Channels\n")
+  cat("---------------------------\n")
+  cat(post_channels,"---------------------------","FCS Markers","---------------------------", post_markers, sep="\n")
+  sink()
+
+  # output fcs
+  if (flag_fcs) {
+    write.FCS(fcs, output)
+  } else {
+    saveRDS(fcs, file = output)
+  }
+}
+
+checkFCS <- function(fcsfile, out_file ="", report="", flag_fcs=FALSE,
+                     marker_sets=list()) {
+  isValid <- F
+  tryCatch({
+    isValid <- isFCSfile(fcsfile)
+  }, error = function(ex) {
+    print(paste(ex))
+  })
+
+  if (isValid) {
+    modifyMarkersFCS(fcsfile, out_file, report, flag_fcs, marker_sets)
+  } else {
+    quit(save = "no", status = 10, runLast = FALSE)
+  }
+}
+
+################################################################################
+################################################################################
+args <- commandArgs(trailingOnly = TRUE)
+flag_fcs <- if (args[3]=="FCS") TRUE else FALSE
+
+items <- args[5:length(args)]
+marker_sets <- list()
+j <- 1
+for (i in seq(1, length(items), 3)) {
+  if (items[i]=="None" || items[i]== "" || items[i]== "i.e.:TLR 6, TLR6PE") {
+    quit(save = "no", status = 11, runLast = FALSE)
+  }
+  if (items[i+1]=="None" || items[i+1]=="" || items[i+1]=="i.e.:TLR6") {
+    quit(save = "no", status = 12, runLast = FALSE)
+  }
+
+  old_names <- strsplit(items[i], ",")[[1]]
+  to_replace <- sapply(old_names, trimws)
+  replacement <- sapply(strsplit(items[i+1], ",")[[1]], trimws)
+  flag_channel <- if (items[i+2]=="C") TRUE else FALSE
+  m_set <- list(to_replace, replacement, flag_channel)
+  marker_sets[[j]] <- m_set
+  j <- j + 1
+}
+
+checkFCS(args[1], args[2], args[4], flag_fcs, marker_sets)