annotate metacyto_histogram.R @ 0:f5526d97056c draft default tip

"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"

#!/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)