Mercurial > repos > azomics > flowsom_tree

comparison FlowSOMGenerateTree.R @ 2:0efc47dba930 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/flowsom_tree commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
author azomics
date Fri, 29 Sep 2023 07:20:10 +0000
parents 54a25f1139b4
children
comparison
equal deleted inserted replaced
1:6c1721e7d0d6 2:0efc47dba930
1 #!/usr/bin/Rscript 1 #!/usr/bin/env Rscript
2 # Module for Galaxy 2 # Module for Galaxy
3 # Generates FlowSOM reference tree 3 # Generates FlowSOM reference tree
4 # with FlowSOM AggregateFlowFrames 4 # with FlowSOM AggregateFlowFrames
5 ###################################################################### 5 ######################################################################
6 # Copyright (c) 2017 Northrop Grumman. 6 # Copyright (c) 2017 Northrop Grumman.
12 # 12 #
13 # 13 #
14 library(FlowSOM) 14 library(FlowSOM)
15 library(flowCore) 15 library(flowCore)
16 16
17 generateTree <- function(ff, output="", columns=list(), cluster=10, xgrid=10, 17 generate_tree <- function(ff, output = "", columns = list(),
18 ygrid=10,plot="", plot_pdf=FALSE, mplot="", flag_def=T, 18 cluster = 10, xgrid = 10,
19 table="", mtable="", flag_meta=FALSE, user_seed=42, 19 ygrid = 10, plot = "", plot_pdf = FALSE,
20 flag_nodesize=F) { 20 mplot = "", flag_def = TRUE,
21 21 table = "", mtable = "",
22 # check default -- if def get all except FSC/SSC 22 flag_meta = FALSE, user_seed = 42,
23 # also check nb of markers/channels and indices 23 flag_nodesize = FALSE) {
24
25 # check default -- if def get all except FSC / SSC
26 # also check nb of markers / channels and indices
24 markers <- colnames(ff) 27 markers <- colnames(ff)
25 print_markers <- as.vector(pData(parameters(ff))$desc) 28 print_markers <- as.vector(pData(parameters(ff))$desc)
26 # Update print_markers if the $P?S not in the FCS file 29 # Update print_markers if the $P?S not in the FCS file
27 for (i in 1:length(print_markers)) { 30 for (i in seq_along(print_markers)) {
28 if (is.na(print_markers[i])) { 31 if (is.na(print_markers[i])) {
29 print_markers[i] <- markers[i] 32 print_markers[i] <- markers[i]
30 } 33 }
31 } 34 }
32 35
33 if (flag_def){ 36 if (flag_def) {
34 channels_to_exclude <- c(grep(markers, pattern="FSC"), 37 channels_to_exclude <- c(grep(markers, pattern = "FSC"),
35 grep(markers, pattern="SSC"), 38 grep(markers, pattern = "SSC"),
36 grep(markers, pattern="Time")) 39 grep(markers, pattern = "Time"))
37 columns <- markers[-channels_to_exclude] 40 columns <- markers[-channels_to_exclude]
38 } 41 }
39 42
40 set.seed(user_seed) 43 set.seed(user_seed)
41 fs <- ReadInput(ff, compensate=F, transform=F, scale=T) 44 fs <- ReadInput(ff, compensate = FALSE, transform = FALSE, scale = TRUE)
42 fs <- BuildSOM(fs, colsToUse = columns, xdim=xgrid, ydim=ygrid) 45 fs <- BuildSOM(fs, colsToUse = columns, xdim = xgrid, ydim = ygrid)
43 fst <- BuildMST(fs, tSNE=T) 46 fst <- BuildMST(fs, tSNE = TRUE)
44 47
45 if (!mplot==""){ 48 if (!mplot == "") {
46 pdf(mplot, useDingbats=FALSE, onefile=TRUE) 49 pdf(mplot, useDingbats = FALSE, onefile = TRUE)
47 for (marker in markers){ 50 for (marker in markers) {
48 PlotMarker(fst, marker) 51 PlotMarker(fst, marker)
49 } 52 }
50 dev.off() 53 dev.off()
51 } 54 }
52 metaC <- metaClustering_consensus(fst$map$codes, k=cluster, seed=user_seed) 55 meta_c <- metaClustering_consensus(
53 56 fst$map$codes,
54 if (!plot==""){ 57 k = cluster,
55 if (flag_nodesize){ 58 seed = user_seed)
56 fst <- UpdateNodeSize(fst, reset=TRUE) 59
57 fst$MST$size <- fst$MST$size/2 60 if (!plot == "") {
61 if (flag_nodesize) {
62 fst <- UpdateNodeSize(fst, reset = TRUE)
63 fst$MST$size <- fst$MST$size / 2
58 } 64 }
59 if (plot_pdf) { 65 if (plot_pdf) {
60 pdf(plot, useDingbats=FALSE) 66 pdf(plot, useDingbats = FALSE)
61 PlotStars(fst, backgroundValues = as.factor(metaC)) 67 PlotStars(fst, backgroundValues = as.factor(meta_c))
62 dev.off() 68 dev.off()
63 } else { 69 } else {
64 png(plot, type="cairo", height=800, width=800) 70 png(plot, type = "cairo", height = 800, width = 800)
65 PlotStars(fst, backgroundValues = as.factor(metaC)) 71 PlotStars(fst, backgroundValues = as.factor(meta_c))
66 dev.off() 72 dev.off()
67 } 73 }
68 } 74 }
69 if (!table==""){ 75 if (!table == "") {
70 m <- matrix(0,nrow=nrow(ff),ncol=1) 76 m <- matrix(0, nrow = nrow(ff), ncol = 1)
71 s <- seq_len(nrow(ff)) 77 s <- seq_len(nrow(ff))
72 if (flag_meta){ 78 if (flag_meta) {
73 m[s,] <- metaC[fst$map$mapping[,1]] 79 m[s, ] <- meta_c[fst$map$mapping[, 1]]
74 } else { 80 } else {
75 m[s,] <- fst$map$mapping[,1] 81 m[s, ] <- fst$map$mapping[, 1]
76 } 82 }
77 colnames(m) <- "FlowSOM" 83 colnames(m) <- "FlowSOM"
78 ff <- cbind2(ff,m) 84 ff <- cbind2(ff, m)
79 out <- exprs(ff) 85 out <- exprs(ff)
80 print_markers <- append(print_markers, "Population") 86 print_markers <- append(print_markers, "Population")
81 colnames(out) <- print_markers 87 colnames(out) <- print_markers
82 write.table(out, file=table, quote=F, row.names=F, col.names=T, sep='\t', 88 write.table(out, file = table, quote = FALSE,
83 append=F) 89 row.names = FALSE, col.names = TRUE, sep = "\t",
84 90 append = FALSE)
85 nb_nodes <- max(fst$map$mapping[,1]) 91
86 mm <- matrix(0, nrow=nb_nodes, ncol=2) 92 nb_nodes <- max(fst$map$mapping[, 1])
93 mm <- matrix(0, nrow = nb_nodes, ncol = 2)
87 ss <- seq_len(nb_nodes) 94 ss <- seq_len(nb_nodes)
88 mm[,1]<- as.character(ss) 95 mm[, 1] <- as.character(ss)
89 mm[ss,2]<- as.character(metaC) 96 mm[ss, 2] <- as.character(meta_c)
90 colnames(mm) <- c("Node", "Meta-Cluster") 97 colnames(mm) <- c("Node", "Meta-Cluster")
91 write.table(mm, file=mtable, quote=F, row.names=F, col.names=T, sep='\t', 98 write.table(mm, file = mtable, quote = FALSE,
92 append=F) 99 row.names = FALSE, col.names = TRUE, sep = "\t",
93 100 append = FALSE)
94 } 101
95 saveRDS(fst, file = output) 102 }
96 } 103 saveRDS(fst, file = output)
97 104 }
98 flowFrameOrFCS <- function(input, output="", columns=list(),cluster=10,xgrid=10, 105
99 ygrid=10,plot="",plot_pdf=FALSE, mplot="", default=T, 106 flow_frame_or_fcs <- function(input, output = "", columns = list(),
100 table="", mtable="", flag_meta=FALSE, user_seed=42, 107 cluster = 10, xgrid = 10,
101 nodesize=FALSE) { 108 ygrid = 10, plot = "", plot_pdf = FALSE,
102 isValid <- F 109 mplot = "", default = TRUE,
103 is_fcs <- F 110 table = "", mtable = "",
104 is_ff <- F 111 flag_meta = FALSE, user_seed = 42,
112 nodesize = FALSE) {
113 is_fcs <- FALSE
114 is_ff <- FALSE
105 ff <- "" 115 ff <- ""
106 tryCatch({ 116 tryCatch({
107 is_fcs <- isFCSfile(input) 117 is_fcs <- isFCSfile(input)
108 }, error = function(ex) { 118 }, error = function(ex) {
109 print(paste(ex)) 119 print(paste(ex))
110 }) 120 })
111 121
112 if (!is_fcs){ 122 if (!is_fcs) {
113 tryCatch({ 123 tryCatch({
114 ff <- readRDS(input) 124 ff <- readRDS(input)
115 is_ff <- T 125 is_ff <- TRUE
116 }, error = function(ex) { 126 }, error = function(ex) {
117 print(paste(ex)) 127 print(paste(ex))
118 }) 128 })
119 } else { 129 } else {
120 ff <- read.FCS(input, transformation=FALSE) 130 ff <- read.FCS(input, transformation = FALSE)
121 } 131 }
122 132
123 if (!is_ff && !is_fcs) { 133 if (!is_ff && !is_fcs) {
124 quit(save = "no", status = 10, runLast = FALSE) 134 quit(save = "no", status = 10, runLast = FALSE)
125 } else { 135 } else {
126 for (cols in columns){ 136 for (cols in columns) {
127 if (cols > length(colnames(ff))){ 137 if (cols > length(colnames(ff))) {
128 quit(save = "no", status = 12, runLast = FALSE) 138 quit(save = "no", status = 12, runLast = FALSE)
129 } 139 }
130 } 140 }
131 generateTree(ff, output, columns, cluster, xgrid, ygrid, plot, plot_pdf, 141 generate_tree(ff, output, columns, cluster, xgrid, ygrid, plot, plot_pdf,
132 mplot, default, table, mtable, flag_meta, user_seed, nodesize) 142 mplot, default, table, mtable, flag_meta, user_seed, nodesize)
133 } 143 }
134 } 144 }
135 145
136 args <- commandArgs(trailingOnly = TRUE) 146 args <- commandArgs(trailingOnly = TRUE)
137 flag_default <- FALSE 147 flag_default <- FALSE
138 columns <- list() 148 columns <- list()
139 149
140 if (args[3] == "" || args[3] == "i.e.:1,2,5") { 150 if (args[3] == "" || args[3] == "i.e.:1,2,5") {
141 flag_default <- TRUE 151 flag_default <- TRUE
142 } else { 152 } else {
143 #rm last X if it's there 153 #rm last X if it's there
144 columns <- as.numeric(strsplit(args[3], ",")[[1]]) 154 columns <- as.numeric(strsplit(args[3], ",")[[1]])
145 for (col in columns){ 155 for (col in columns) {
146 if (is.na(col)){ 156 if (is.na(col)) {
147 quit(save = "no", status = 11, runLast = FALSE) 157 quit(save = "no", status = 11, runLast = FALSE)
148 } 158 }
149 } 159 }
150 } 160 }
151 161
152 cluster <- 10 162 cluster <- 10
153 if (!args[4] == ""){ 163 if (!args[4] == "") {
154 if (!is.na(as.integer(args[4]))){ 164 if (!is.na(as.integer(args[4]))) {
155 cluster <- as.integer(args[4]) 165 cluster <- as.integer(args[4])
156 } else { 166 } else {
157 quit(save = "no", status = 13, runLast = FALSE) 167 quit(save = "no", status = 13, runLast = FALSE)
158 } 168 }
159 } 169 }
160 170
161 xgrid <- 10 171 xgrid <- 10
162 if (!args[5] == ""){ 172 if (!args[5] == "") {
163 if (!is.na(as.integer(args[5]))){ 173 if (!is.na(as.integer(args[5]))) {
164 cluster <- as.integer(args[5]) 174 cluster <- as.integer(args[5])
165 } else { 175 } else {
166 quit(save = "no", status = 14, runLast = FALSE) 176 quit(save = "no", status = 14, runLast = FALSE)
167 } 177 }
168 } 178 }
169 179
170 ygrid <- 10 180 ygrid <- 10
171 if (!args[6] == ""){ 181 if (!args[6] == "") {
172 if (!is.na(as.integer(args[6]))){ 182 if (!is.na(as.integer(args[6]))) {
173 cluster <- as.integer(args[6]) 183 cluster <- as.integer(args[6])
174 } else { 184 } else {
175 quit(save = "no", status = 14, runLast = FALSE) 185 quit(save = "no", status = 14, runLast = FALSE)
176 } 186 }
177 } 187 }
178 seed <- 42 188 seed <- 42
179 if (!args[7]==""){ 189 if (!args[7] == "") {
180 if (!is.na(as.integer(args[7]))){ 190 if (!is.na(as.integer(args[7]))) {
181 seed <- as.integer(args[7]) 191 seed <- as.integer(args[7])
182 } else { 192 } else {
183 quit(save = "no", status = 15, runLast = FALSE) 193 quit(save = "no", status = 15, runLast = FALSE)
184 } 194 }
185 } 195 }
186 196
187 plot <- "" 197 plot <- ""
188 mplot <- "" 198 mplot <- ""
191 mtable <- "" 201 mtable <- ""
192 flag_meta <- FALSE 202 flag_meta <- FALSE
193 nodesize <- FALSE 203 nodesize <- FALSE
194 nb_args <- length(args) 204 nb_args <- length(args)
195 205
196 if (nb_args==16) { 206 if (nb_args == 16) {
197 plot <- args[8] 207 plot <- args[8]
198 if (args[9]=='PDF') { 208 if (args[9] == "PDF") {
199 plot_pdf <- TRUE 209 plot_pdf <- TRUE
200 } 210 }
201 nodesize <- args[10] 211 nodesize <- args[10]
202 mplot <- args[11] 212 mplot <- args[11]
203 table <- args[13] 213 table <- args[13]
204 mtable <- args[14] 214 mtable <- args[14]
205 if (args[12]=='meta'){ 215 if (args[12] == "meta") {
206 flag_meta<-TRUE 216 flag_meta <- TRUE
207 } 217 }
208 } else if (nb_args==15){ 218 } else if (nb_args == 15) {
209 plot <- args[8] 219 plot <- args[8]
210 if (args[9]=='PDF') { 220 if (args[9] == "PDF") {
211 plot_pdf <- TRUE 221 plot_pdf <- TRUE
212 } 222 }
213 nodesize <- args[10] 223 nodesize <- args[10]
214 table <- args[12] 224 table <- args[12]
215 mtable <- args[13] 225 mtable <- args[13]
216 if (args[11]=='meta'){ 226 if (args[11] == "meta") {
217 flag_meta<-TRUE 227 flag_meta <- TRUE
218 } 228 }
219 } else if (nb_args==13) { 229 } else if (nb_args == 13) {
220 mplot <- args[8] 230 mplot <- args[8]
221 table <- args[10] 231 table <- args[10]
222 mtable <- args[11] 232 mtable <- args[11]
223 if (args[9]=='meta'){ 233 if (args[9] == "meta") {
224 flag_meta<-TRUE 234 flag_meta <- TRUE
225 } 235 }
226 } else if (nb_args==12) { 236 } else if (nb_args == 12) {
227 table <- args[9] 237 table <- args[9]
228 mtable <- args[10] 238 mtable <- args[10]
229 if (args[8]=='meta'){ 239 if (args[8] == "meta") {
230 flag_meta<-TRUE 240 flag_meta <- TRUE
231 } 241 }
232 } else if (nb_args==11) { 242 } else if (nb_args == 11) {
233 plot <- args[8] 243 plot <- args[8]
234 if (args[9]=='PDF') { 244 if (args[9] == "PDF") {
235 plot_pdf <- TRUE 245 plot_pdf <- TRUE
236 } 246 }
237 nodesize <- args[10] 247 nodesize <- args[10]
238 mplot <- args[11] 248 mplot <- args[11]
239 } else if (nb_args==10) { 249 } else if (nb_args == 10) {
240 plot <- args[8] 250 plot <- args[8]
241 if (args[9]=='PDF') { 251 if (args[9] == "PDF") {
242 plot_pdf <- TRUE 252 plot_pdf <- TRUE
243 } 253 }
244 nodesize <- args[10] 254 nodesize <- args[10]
245 } else if (nb_args==8){ 255 } else if (nb_args == 8) {
246 mplot <- args[8] 256 mplot <- args[8]
247 } 257 }
248 258
249 flowFrameOrFCS(args[1], args[2], columns, cluster, xgrid, ygrid, plot, plot_pdf, 259 flow_frame_or_fcs(args[1], args[2],
250 mplot, flag_default, table, mtable, flag_meta, seed, nodesize) 260 columns, cluster, xgrid, ygrid, plot, plot_pdf,
261 mplot, flag_default, table, mtable, flag_meta, seed, nodesize)