--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metacyto_histogram.R	Thu Jul 29 22:15:11 2021 +0000
@@ -0,0 +1,123 @@
+#!/usr/bin/env Rscript
+######################################################################
+#                  Copyright (c) 2018 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Version 1 - January 2018
+# Author: Cristel Thomas
+#
+#
+
+library(flowCore)
+library(MetaCyto)
+
+check_cluster_def <- function(cl_def) {
+  if (cl_def == "" || cl_def == "None") {
+    quit(save = "no", status = 12, runLast = FALSE)
+  } else {
+    tmp <- gsub(" ", "", cl_def, fixed = TRUE)
+    clean_def <- gsub(",", "|", tmp, fixed = TRUE)
+    return(clean_def)
+  }
+}
+
+generate_plots <- function(fpath = "", fname = "", gates = vector(), outdir = "", uc = "",
+                          flag_pdf = F) {
+  dir.create(outdir)
+  ff <- read.FCS(fpath, truncate_max_range = F)
+  markers <- markerFinder(ff)
+  colnames(ff@exprs) <- markers
+
+  sc <- searchCluster(fcsFrame = ff, clusterLabel = gates)
+
+  if (length(gates) == length(sc$clusterList)) {
+    sink(uc)
+    cat("All provided cluster definition were used.")
+    sink()
+  } else {
+    unused_cluster <- setdiff(gates, names(sc$clusterList))
+    write.table(unused_cluster, uc, quote = F, row.names = F, col.names = F)
+  }
+
+  groupname <- unlist(strsplit(fname, ".fcs"))[[1]]
+  extension <- if (flag_pdf) "plot.pdf" else "plot.png"
+  for (i in seq_len(length(sc$clusterList))) {
+    gate <- gsub("|", "", names(sc$clusterList[i]), fixed = T)
+    plotname <- paste(c(groupname, gate, extension), collapse = "_")
+    outplot <- file.path(outdir, plotname)
+    if (flag_pdf) {
+      pdf(outplot, useDingbats = F, onefile = T)
+      par(mfrow = c(2, 2))
+      for (j in seq_len(length(markers))) {
+        if (markers[[j]] != "SAMPLE_ID" && markers[[j]] != "TIME") {
+          plot_title <- paste0(markers[[j]], ", cluster definition:\n", gate)
+          x_all <- ff@exprs[, markers[[j]]]
+          b <- seq(min(x_all), max(x_all), ((max(x_all) - min(x_all)) / 100))
+          subset <- ff@exprs[sc$clusterList[[i]], markers[[j]]]
+          hist(x_all, col = rgb(0, 0, 0), xlab = markers[[j]], breaks = b, freq = T,
+               border = F, main = plot_title)
+          hist(subset, add = T, breaks = b, col = rgb(1, 0, 0), freq = T, border = F)
+          if (markers[[j]] %in% names(sc$cutoff)) {
+            abline(v = sc$cutoff[markers[[j]]])
+          }
+        }
+      }
+      dev.off()
+    } else {
+      markers_ct <- length(markers) - length(grep(x = markers, pattern = "SAMPLE_ID|TIME"))
+      nb_rows <- ceiling(markers_ct / 2)
+      h <- nb_rows * 400
+      png(outplot, type = "cairo", height = h, width = 800)
+      par(mfrow = c(nb_rows, 2))
+      for (j in seq_len(length(markers))) {
+        if (markers[[j]] != "SAMPLE_ID" && markers[[j]] != "TIME") {
+          plot_title <- paste0(markers[[j]], ", cluster definition:\n", gate)
+          x_all <- ff@exprs[, markers[[j]]]
+          b <- seq(min(x_all), max(x_all), ((max(x_all) - min(x_all)) / 100))
+          subset <- ff@exprs[sc$clusterList[[i]], markers[[j]]]
+          hist(x_all, col = rgb(0, 0, 0), xlab = markers[[j]], breaks = b, freq = T,
+               border = F, main = plot_title)
+          hist(subset, add = T, breaks = b, col = rgb(1, 0, 0), freq = T, border = F)
+          if (markers[[j]] %in% names(sc$cutoff)) {
+            abline(v = sc$cutoff[markers[[j]]])
+          }
+        }
+      }
+      dev.off()
+    }
+  }
+}
+
+check_fcs_file <- function(inputf="", inputn="", clusters=vector(),
+                         output_dir = "", unused = "", flag = F) {
+  is_valid <- FALSE
+  tryCatch({
+    is_valid <- isFCSfile(inputf)
+  }, error = function(ex) {
+    print(paste("Input file is not a valid FCS file.", ex))
+  })
+  if (is_valid) {
+    generate_plots(inputf, inputn, clusters, output_dir, unused, flag)
+  } else {
+    quit(save = "no", status = 12, runLast = FALSE)
+  }
+}
+
+################################################################################
+################################################################################
+args <- commandArgs(trailingOnly = TRUE)
+
+gates <- vector()
+if (args[6] == "F") {
+  ## obvs deal with it if file
+  cluster_file <- read.table(args[7], header = F, colClasses = "character")
+  gates <- unlist(cluster_file)
+} else {
+  cl_df <- args[7:length(args)]
+  gates <- sapply(cl_df, check_cluster_def)
+}
+
+flag_pdf <- if (args[5] == "PDF") TRUE else FALSE
+gate_list <- toupper(gates)
+check_fcs_file(args[1], args[2], gate_list, args[3], args[4], flag_pdf)