Mercurial > repos > azomics > flowviz_density_plots

comparison FCSflowViz.R @ 0:23c0af6be9a7 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/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
author azomics
date Mon, 22 Jun 2020 20:48:47 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:23c0af6be9a7
1 #!/usr/bin/Rscript
2 # Stacked 1D Density Plot Module for Galaxy
3 # flowviz
4 ######################################################################
5 # Copyright (c) 2016 Northrop Grumman.
6 # All rights reserved.
7 ######################################################################
8 #
9 # Version 1
10 # Cristel Thomas
11 #
12 #
13
14 library(flowViz)
15 library(methods)
16
17 generateStackedPlots <- function(fs, chans=list(), output="", flag_pdf=FALSE) {
18 h <- 800
19 w <- 1200
20 if (length(fs@colnames)>8){
21 h <- 1200
22 w <- 1600
23 }
24 channels_to_plot <- fs@colnames
25 if (length(chans) > 0){
26 channels_to_plot <- fs@colnames[chans]
27 }
28
29 if (flag_pdf) {
30 pdf(output, useDingbats=FALSE, onefile=TRUE)
31 print({
32 densityplot(~., fs, channels = channels_to_plot)
33 })
34 dev.off()
35 } else {
36 png(output, type="cairo", height=h, width=w)
37 print({
38 densityplot(~., fs, channels = channels_to_plot)
39 })
40 dev.off()
41 }
42 }
43
44 checkFlowSet <- function(fcsfiles, newnames, channels=list(), out_file ="",
45 flag_pdf=FALSE) {
46
47 isValid <- F
48 markerCheck <- T
49
50 for (i in 1:length(fcsfiles)){
51 is_file_valid <- F
52 tryCatch({
53 fcs <- read.FCS(fcsfiles[i], transformation=FALSE)
54 is_file_valid <- T
55 }, error = function(ex) {
56 print(paste(ex))
57 })
58 if (i == 1) {
59 m1 <- as.vector(pData(parameters(fcs))$desc)
60 } else {
61 m2 <- as.vector(pData(parameters(fcs))$desc)
62 if (is.na(all(m1==m2))) {
63 mm1 <- is.na(m1)
64 mm2 <- is.na(m2)
65 if (all(mm1==mm2)){
66 if (!all(m1==m2, na.rm=TRUE)){
67 markerCheck <- F
68 }
69 } else {
70 markerCheck <- F
71 }
72 } else if (!all(m1==m2)) {
73 markerCheck <- F
74 }
75 }
76 }
77 if (markerCheck) {
78 isValid <- T
79 } else {
80 quit(save = "no", status = 12, runLast = FALSE)
81 }
82
83 if (isValid) {
84 fs <- read.flowSet(files=fcsfiles, transformation=FALSE)
85 fs@phenoData@data$name <- newnames
86 generateStackedPlots(fs, channels, out_file, flag_pdf)
87 } else {
88 quit(save = "no", status = 12, runLast = FALSE)
89 }
90 }
91
92 args <- commandArgs(trailingOnly = TRUE)
93 channels <- list()
94 flag_pdf <- FALSE
95
96 if (args[1]=="None") {
97 flag_default <- TRUE
98 } else {
99 if (args[1] == "i.e.:1,3,4"){
100 flag_default <- TRUE
101 } else {
102 channels <- as.numeric(strsplit(args[1], ",")[[1]])
103 for (channel in channels){
104 if (is.na(channel)){
105 quit(save = "no", status = 11, runLast = FALSE)
106 }
107 }
108 }
109 }
110
111 if (args[3] == "PDF"){
112 flag_pdf <- TRUE
113 }
114
115 nb_files <- (length(args) - 3) / 2
116 fcsfiles <- character(nb_files)
117 newnames <- character(nb_files)
118 j <- 1
119 ## get files and file names
120 for (i in 4:length(args)) {
121 if (!i%%2){
122 fcsfiles[[j]] <- args[i]
123 newnames[[j]] <- args[i+1]
124 j <- j + 1
125 }
126 }
127
128 checkFlowSet(fcsfiles, newnames, channels, args[2], flag_pdf)