Mercurial > repos > azomics > edit_fcs_markers

comparison editFCSmarkers.R @ 0:02b2412598b6 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/edit_fcs_marker commit 05dd0e3c6e8eff9383d3f755ade2ca8557ebe7e7"
author azomics
date Mon, 22 Jun 2020 20:07:30 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:02b2412598b6
1 #!/usr/bin/Rscript
2 # modify channels and marker names in FCS
3 #
4 ######################################################################
5 # Copyright (c) 2017 Northrop Grumman.
6 # All rights reserved.
7 ######################################################################
8 #
9 # Cristel Thomas
10 # Version 2 - May 2018
11 # Modified to take in marker/channel names by name rather than index
12 #
13 library(flowCore)
14
15 checkCandM <- function(m_set, channels=vector(), markers=vector()){
16 if (m_set[[3]]){
17 in_file <- m_set[[1]] %in% channels
18 } else {
19 in_file <- m_set[[1]] %in% markers
20 }
21 if (sum(in_file)==0) {
22 warning("Given original columns are either not in the channels or in the markers of the read object. Will fail.")
23 return(FALSE)
24 }
25 return(TRUE)
26 }
27
28 modifyMarkersFCS <- function(input, output="", report="", flag_fcs=F,
29 marker_sets=list()) {
30
31 fcs <- read.FCS(input, transformation=F)
32 original_channels <- colnames(fcs)
33 original_markers <- as.vector(pData(parameters(fcs))$desc)
34 nb <- length(original_channels)
35 ## check if markers are in FCS files
36 check_markers <- sapply(marker_sets, checkCandM, channels=original_channels,
37 markers=original_markers)
38 if (sum(check_markers)==0) {
39 quit(save = "no", status = 13, runLast = FALSE)
40 }
41
42 post_channels <- colnames(fcs)
43 post_markers <- as.vector(pData(parameters(fcs))$desc)
44
45 for (m_set in marker_sets) {
46 if (m_set[[3]]){
47 chan_to_replace <- post_channels %in% m_set[[1]]
48 for (i in 1:nb){
49 if (chan_to_replace[[i]]){
50 post_channels[[i]] <- m_set[[2]][[match(post_channels[[i]], m_set[[1]])[1]]]
51 }
52 }
53 } else {
54 marker_to_replace <- post_markers %in% m_set[[1]]
55 for (i in 1:nb){
56 if (marker_to_replace[[i]]){
57 post_markers[[i]] <- m_set[[2]][[match(post_markers[[i]], m_set[[1]])[1]]]
58 pm <- paste("$P", as.character(i), "S", sep="")
59 fcs@description[[pm]] <- post_markers[[i]]
60 }
61 }
62 }
63 }
64
65 colnames(fcs) <- post_channels
66 pData(parameters(fcs))$desc <- post_markers
67
68 # write report
69 sink(report)
70 cat("###########################\n")
71 cat("## BEFORE RENAMING ##\n")
72 cat("###########################\nFCS Channels\n")
73 cat("---------------------------\n")
74 cat(original_channels,"---------------------------", "FCS Markers","---------------------------",original_markers, sep="\n")
75 cat("\n###########################\n")
76 cat("## AFTER RENAMING ##\n")
77 cat("###########################\nFCS Channels\n")
78 cat("---------------------------\n")
79 cat(post_channels,"---------------------------","FCS Markers","---------------------------", post_markers, sep="\n")
80 sink()
81
82 # output fcs
83 if (flag_fcs) {
84 write.FCS(fcs, output)
85 } else {
86 saveRDS(fcs, file = output)
87 }
88 }
89
90 checkFCS <- function(fcsfile, out_file ="", report="", flag_fcs=FALSE,
91 marker_sets=list()) {
92 isValid <- F
93 tryCatch({
94 isValid <- isFCSfile(fcsfile)
95 }, error = function(ex) {
96 print(paste(ex))
97 })
98
99 if (isValid) {
100 modifyMarkersFCS(fcsfile, out_file, report, flag_fcs, marker_sets)
101 } else {
102 quit(save = "no", status = 10, runLast = FALSE)
103 }
104 }
105
106 ################################################################################
107 ################################################################################
108 args <- commandArgs(trailingOnly = TRUE)
109 flag_fcs <- if (args[3]=="FCS") TRUE else FALSE
110
111 items <- args[5:length(args)]
112 marker_sets <- list()
113 j <- 1
114 for (i in seq(1, length(items), 3)) {
115 if (items[i]=="None" || items[i]== "" || items[i]== "i.e.:TLR 6, TLR6PE") {
116 quit(save = "no", status = 11, runLast = FALSE)
117 }
118 if (items[i+1]=="None" || items[i+1]=="" || items[i+1]=="i.e.:TLR6") {
119 quit(save = "no", status = 12, runLast = FALSE)
120 }
121
122 old_names <- strsplit(items[i], ",")[[1]]
123 to_replace <- sapply(old_names, trimws)
124 replacement <- sapply(strsplit(items[i+1], ",")[[1]], trimws)
125 flag_channel <- if (items[i+2]=="C") TRUE else FALSE
126 m_set <- list(to_replace, replacement, flag_channel)
127 marker_sets[[j]] <- m_set
128 j <- j + 1
129 }
130
131 checkFCS(args[1], args[2], args[4], flag_fcs, marker_sets)