Mercurial > repos > azomics > flowsom_tree

comparison FlowSOMGenerateTree.R @ 0:54a25f1139b4 draft

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
author azomics
date Tue, 23 Jun 2020 12:46:08 -0400
parents
children 0efc47dba930
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-1:000000000000 0:54a25f1139b4
1 #!/usr/bin/Rscript
2 # Module for Galaxy
3 # Generates FlowSOM reference tree
4 # with FlowSOM AggregateFlowFrames
5 ######################################################################
6 # Copyright (c) 2017 Northrop Grumman.
7 # All rights reserved.
8 ######################################################################
9 #
10 # Version 1
11 # Cristel Thomas
12 #
13 #
14 library(FlowSOM)
15 library(flowCore)
16
17 generateTree <- function(ff, output="", columns=list(), cluster=10, xgrid=10,
18 ygrid=10,plot="", plot_pdf=FALSE, mplot="", flag_def=T,
19 table="", mtable="", flag_meta=FALSE, user_seed=42,
20 flag_nodesize=F) {
21
22 # check default -- if def get all except FSC/SSC
23 # also check nb of markers/channels and indices
24 markers <- colnames(ff)
25 print_markers <- as.vector(pData(parameters(ff))$desc)
26 # Update print_markers if the $P?S not in the FCS file
27 for (i in 1:length(print_markers)) {
28 if (is.na(print_markers[i])) {
29 print_markers[i] <- markers[i]
30 }
31 }
32
33 if (flag_def){
34 channels_to_exclude <- c(grep(markers, pattern="FSC"),
35 grep(markers, pattern="SSC"),
36 grep(markers, pattern="Time"))
37 columns <- markers[-channels_to_exclude]
38 }
39
40 set.seed(user_seed)
41 fs <- ReadInput(ff, compensate=F, transform=F, scale=T)
42 fs <- BuildSOM(fs, colsToUse = columns, xdim=xgrid, ydim=ygrid)
43 fst <- BuildMST(fs, tSNE=T)
44
45 if (!mplot==""){
46 pdf(mplot, useDingbats=FALSE, onefile=TRUE)
47 for (marker in markers){
48 PlotMarker(fst, marker)
49 }
50 dev.off()
51 }
52 metaC <- metaClustering_consensus(fst$map$codes, k=cluster, seed=user_seed)
53
54 if (!plot==""){
55 if (flag_nodesize){
56 fst <- UpdateNodeSize(fst, reset=TRUE)
57 fst$MST$size <- fst$MST$size/2
58 }
59 if (plot_pdf) {
60 pdf(plot, useDingbats=FALSE)
61 PlotStars(fst, backgroundValues = as.factor(metaC))
62 dev.off()
63 } else {
64 png(plot, type="cairo", height=800, width=800)
65 PlotStars(fst, backgroundValues = as.factor(metaC))
66 dev.off()
67 }
68 }
69 if (!table==""){
70 m <- matrix(0,nrow=nrow(ff),ncol=1)
71 s <- seq_len(nrow(ff))
72 if (flag_meta){
73 m[s,] <- metaC[fst$map$mapping[,1]]
74 } else {
75 m[s,] <- fst$map$mapping[,1]
76 }
77 colnames(m) <- "FlowSOM"
78 ff <- cbind2(ff,m)
79 out <- exprs(ff)
80 print_markers <- append(print_markers, "Population")
81 colnames(out) <- print_markers
82 write.table(out, file=table, quote=F, row.names=F, col.names=T, sep='\t',
83 append=F)
84
85 nb_nodes <- max(fst$map$mapping[,1])
86 mm <- matrix(0, nrow=nb_nodes, ncol=2)
87 ss <- seq_len(nb_nodes)
88 mm[,1]<- as.character(ss)
89 mm[ss,2]<- as.character(metaC)
90 colnames(mm) <- c("Node", "Meta-Cluster")
91 write.table(mm, file=mtable, quote=F, row.names=F, col.names=T, sep='\t',
92 append=F)
93
94 }
95 saveRDS(fst, file = output)
96 }
97
98 flowFrameOrFCS <- function(input, output="", columns=list(),cluster=10,xgrid=10,
99 ygrid=10,plot="",plot_pdf=FALSE, mplot="", default=T,
100 table="", mtable="", flag_meta=FALSE, user_seed=42,
101 nodesize=FALSE) {
102 isValid <- F
103 is_fcs <- F
104 is_ff <- F
105 ff <- ""
106 tryCatch({
107 is_fcs <- isFCSfile(input)
108 }, error = function(ex) {
109 print(paste(ex))
110 })
111
112 if (!is_fcs){
113 tryCatch({
114 ff <- readRDS(input)
115 is_ff <- T
116 }, error = function(ex) {
117 print(paste(ex))
118 })
119 } else {
120 ff <- read.FCS(input, transformation=FALSE)
121 }
122
123 if (!is_ff && !is_fcs) {
124 quit(save = "no", status = 10, runLast = FALSE)
125 } else {
126 for (cols in columns){
127 if (cols > length(colnames(ff))){
128 quit(save = "no", status = 12, runLast = FALSE)
129 }
130 }
131 generateTree(ff, output, columns, cluster, xgrid, ygrid, plot, plot_pdf,
132 mplot, default, table, mtable, flag_meta, user_seed, nodesize)
133 }
134 }
135
136 args <- commandArgs(trailingOnly = TRUE)
137 flag_default <- FALSE
138 columns <- list()
139
140 if (args[3] == "" || args[3] == "i.e.:1,2,5") {
141 flag_default <- TRUE
142 } else {
143 #rm last X if it's there
144 columns <- as.numeric(strsplit(args[3], ",")[[1]])
145 for (col in columns){
146 if (is.na(col)){
147 quit(save = "no", status = 11, runLast = FALSE)
148 }
149 }
150 }
151
152 cluster <- 10
153 if (!args[4] == ""){
154 if (!is.na(as.integer(args[4]))){
155 cluster <- as.integer(args[4])
156 } else {
157 quit(save = "no", status = 13, runLast = FALSE)
158 }
159 }
160
161 xgrid <- 10
162 if (!args[5] == ""){
163 if (!is.na(as.integer(args[5]))){
164 cluster <- as.integer(args[5])
165 } else {
166 quit(save = "no", status = 14, runLast = FALSE)
167 }
168 }
169
170 ygrid <- 10
171 if (!args[6] == ""){
172 if (!is.na(as.integer(args[6]))){
173 cluster <- as.integer(args[6])
174 } else {
175 quit(save = "no", status = 14, runLast = FALSE)
176 }
177 }
178 seed <- 42
179 if (!args[7]==""){
180 if (!is.na(as.integer(args[7]))){
181 seed <- as.integer(args[7])
182 } else {
183 quit(save = "no", status = 15, runLast = FALSE)
184 }
185 }
186
187 plot <- ""
188 mplot <- ""
189 plot_pdf <- FALSE
190 table <- ""
191 mtable <- ""
192 flag_meta <- FALSE
193 nodesize <- FALSE
194 nb_args <- length(args)
195
196 if (nb_args==16) {
197 plot <- args[8]
198 if (args[9]=='PDF') {
199 plot_pdf <- TRUE
200 }
201 nodesize <- args[10]
202 mplot <- args[11]
203 table <- args[13]
204 mtable <- args[14]
205 if (args[12]=='meta'){
206 flag_meta<-TRUE
207 }
208 } else if (nb_args==15){
209 plot <- args[8]
210 if (args[9]=='PDF') {
211 plot_pdf <- TRUE
212 }
213 nodesize <- args[10]
214 table <- args[12]
215 mtable <- args[13]
216 if (args[11]=='meta'){
217 flag_meta<-TRUE
218 }
219 } else if (nb_args==13) {
220 mplot <- args[8]
221 table <- args[10]
222 mtable <- args[11]
223 if (args[9]=='meta'){
224 flag_meta<-TRUE
225 }
226 } else if (nb_args==12) {
227 table <- args[9]
228 mtable <- args[10]
229 if (args[8]=='meta'){
230 flag_meta<-TRUE
231 }
232 } else if (nb_args==11) {
233 plot <- args[8]
234 if (args[9]=='PDF') {
235 plot_pdf <- TRUE
236 }
237 nodesize <- args[10]
238 mplot <- args[11]
239 } else if (nb_args==10) {
240 plot <- args[8]
241 if (args[9]=='PDF') {
242 plot_pdf <- TRUE
243 }
244 nodesize <- args[10]
245 } else if (nb_args==8){
246 mplot <- args[8]
247 }
248
249 flowFrameOrFCS(args[1], args[2], columns, cluster, xgrid, ygrid, plot, plot_pdf,
250 mplot, flag_default, table, mtable, flag_meta, seed, nodesize)