Mercurial > repos > azomics > flowsom_tree
changeset 2:0efc47dba930 draft default tip
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 | 6c1721e7d0d6 |
| children | |
| files | FlowSOMGenerateTree.R FlowSOMGenerateTree.xml |
| diffstat | 2 files changed, 111 insertions(+), 99 deletions(-) [+] |
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--- a/FlowSOMGenerateTree.R Mon Jul 06 19:50:37 2020 -0400 +++ b/FlowSOMGenerateTree.R Fri Sep 29 07:20:10 2023 +0000 @@ -1,4 +1,4 @@ -#!/usr/bin/Rscript +#!/usr/bin/env Rscript # Module for Galaxy # Generates FlowSOM reference tree # with FlowSOM AggregateFlowFrames @@ -14,173 +14,183 @@ library(FlowSOM) library(flowCore) -generateTree <- function(ff, output="", columns=list(), cluster=10, xgrid=10, - ygrid=10,plot="", plot_pdf=FALSE, mplot="", flag_def=T, - table="", mtable="", flag_meta=FALSE, user_seed=42, - flag_nodesize=F) { +generate_tree <- function(ff, output = "", columns = list(), + cluster = 10, xgrid = 10, + ygrid = 10, plot = "", plot_pdf = FALSE, + mplot = "", flag_def = TRUE, + table = "", mtable = "", + flag_meta = FALSE, user_seed = 42, + flag_nodesize = FALSE) { - # check default -- if def get all except FSC/SSC - # also check nb of markers/channels and indices + # check default -- if def get all except FSC / SSC + # also check nb of markers / channels and indices markers <- colnames(ff) print_markers <- as.vector(pData(parameters(ff))$desc) # Update print_markers if the $P?S not in the FCS file - for (i in 1:length(print_markers)) { + for (i in seq_along(print_markers)) { if (is.na(print_markers[i])) { print_markers[i] <- markers[i] } } - if (flag_def){ - channels_to_exclude <- c(grep(markers, pattern="FSC"), - grep(markers, pattern="SSC"), - grep(markers, pattern="Time")) + if (flag_def) { + channels_to_exclude <- c(grep(markers, pattern = "FSC"), + grep(markers, pattern = "SSC"), + grep(markers, pattern = "Time")) columns <- markers[-channels_to_exclude] } set.seed(user_seed) - fs <- ReadInput(ff, compensate=F, transform=F, scale=T) - fs <- BuildSOM(fs, colsToUse = columns, xdim=xgrid, ydim=ygrid) - fst <- BuildMST(fs, tSNE=T) + fs <- ReadInput(ff, compensate = FALSE, transform = FALSE, scale = TRUE) + fs <- BuildSOM(fs, colsToUse = columns, xdim = xgrid, ydim = ygrid) + fst <- BuildMST(fs, tSNE = TRUE) - if (!mplot==""){ - pdf(mplot, useDingbats=FALSE, onefile=TRUE) - for (marker in markers){ + if (!mplot == "") { + pdf(mplot, useDingbats = FALSE, onefile = TRUE) + for (marker in markers) { PlotMarker(fst, marker) } dev.off() } - metaC <- metaClustering_consensus(fst$map$codes, k=cluster, seed=user_seed) + meta_c <- metaClustering_consensus( + fst$map$codes, + k = cluster, + seed = user_seed) - if (!plot==""){ - if (flag_nodesize){ - fst <- UpdateNodeSize(fst, reset=TRUE) - fst$MST$size <- fst$MST$size/2 + if (!plot == "") { + if (flag_nodesize) { + fst <- UpdateNodeSize(fst, reset = TRUE) + fst$MST$size <- fst$MST$size / 2 } if (plot_pdf) { - pdf(plot, useDingbats=FALSE) - PlotStars(fst, backgroundValues = as.factor(metaC)) + pdf(plot, useDingbats = FALSE) + PlotStars(fst, backgroundValues = as.factor(meta_c)) dev.off() } else { - png(plot, type="cairo", height=800, width=800) - PlotStars(fst, backgroundValues = as.factor(metaC)) + png(plot, type = "cairo", height = 800, width = 800) + PlotStars(fst, backgroundValues = as.factor(meta_c)) dev.off() } } - if (!table==""){ - m <- matrix(0,nrow=nrow(ff),ncol=1) + if (!table == "") { + m <- matrix(0, nrow = nrow(ff), ncol = 1) s <- seq_len(nrow(ff)) - if (flag_meta){ - m[s,] <- metaC[fst$map$mapping[,1]] + if (flag_meta) { + m[s, ] <- meta_c[fst$map$mapping[, 1]] } else { - m[s,] <- fst$map$mapping[,1] + m[s, ] <- fst$map$mapping[, 1] } colnames(m) <- "FlowSOM" - ff <- cbind2(ff,m) + ff <- cbind2(ff, m) out <- exprs(ff) print_markers <- append(print_markers, "Population") colnames(out) <- print_markers - write.table(out, file=table, quote=F, row.names=F, col.names=T, sep='\t', - append=F) + write.table(out, file = table, quote = FALSE, + row.names = FALSE, col.names = TRUE, sep = "\t", + append = FALSE) - nb_nodes <- max(fst$map$mapping[,1]) - mm <- matrix(0, nrow=nb_nodes, ncol=2) + nb_nodes <- max(fst$map$mapping[, 1]) + mm <- matrix(0, nrow = nb_nodes, ncol = 2) ss <- seq_len(nb_nodes) - mm[,1]<- as.character(ss) - mm[ss,2]<- as.character(metaC) + mm[, 1] <- as.character(ss) + mm[ss, 2] <- as.character(meta_c) colnames(mm) <- c("Node", "Meta-Cluster") - write.table(mm, file=mtable, quote=F, row.names=F, col.names=T, sep='\t', - append=F) + write.table(mm, file = mtable, quote = FALSE, + row.names = FALSE, col.names = TRUE, sep = "\t", + append = FALSE) } - saveRDS(fst, file = output) + saveRDS(fst, file = output) } -flowFrameOrFCS <- function(input, output="", columns=list(),cluster=10,xgrid=10, - ygrid=10,plot="",plot_pdf=FALSE, mplot="", default=T, - table="", mtable="", flag_meta=FALSE, user_seed=42, - nodesize=FALSE) { - isValid <- F - is_fcs <- F - is_ff <- F +flow_frame_or_fcs <- function(input, output = "", columns = list(), + cluster = 10, xgrid = 10, + ygrid = 10, plot = "", plot_pdf = FALSE, + mplot = "", default = TRUE, + table = "", mtable = "", + flag_meta = FALSE, user_seed = 42, + nodesize = FALSE) { + is_fcs <- FALSE + is_ff <- FALSE ff <- "" tryCatch({ is_fcs <- isFCSfile(input) - }, error = function(ex) { + }, error = function(ex) { print(paste(ex)) }) - if (!is_fcs){ + if (!is_fcs) { tryCatch({ ff <- readRDS(input) - is_ff <- T - }, error = function(ex) { + is_ff <- TRUE + }, error = function(ex) { print(paste(ex)) }) } else { - ff <- read.FCS(input, transformation=FALSE) + ff <- read.FCS(input, transformation = FALSE) } if (!is_ff && !is_fcs) { - quit(save = "no", status = 10, runLast = FALSE) + quit(save = "no", status = 10, runLast = FALSE) } else { - for (cols in columns){ - if (cols > length(colnames(ff))){ - quit(save = "no", status = 12, runLast = FALSE) + for (cols in columns) { + if (cols > length(colnames(ff))) { + quit(save = "no", status = 12, runLast = FALSE) } } - generateTree(ff, output, columns, cluster, xgrid, ygrid, plot, plot_pdf, - mplot, default, table, mtable, flag_meta, user_seed, nodesize) + generate_tree(ff, output, columns, cluster, xgrid, ygrid, plot, plot_pdf, + mplot, default, table, mtable, flag_meta, user_seed, nodesize) } } -args <- commandArgs(trailingOnly = TRUE) +args <- commandArgs(trailingOnly = TRUE) flag_default <- FALSE columns <- list() -if (args[3] == "" || args[3] == "i.e.:1,2,5") { +if (args[3] == "" || args[3] == "i.e.:1,2,5") { flag_default <- TRUE } else { #rm last X if it's there columns <- as.numeric(strsplit(args[3], ",")[[1]]) - for (col in columns){ - if (is.na(col)){ - quit(save = "no", status = 11, runLast = FALSE) + for (col in columns) { + if (is.na(col)) { + quit(save = "no", status = 11, runLast = FALSE) } } } cluster <- 10 -if (!args[4] == ""){ - if (!is.na(as.integer(args[4]))){ +if (!args[4] == "") { + if (!is.na(as.integer(args[4]))) { cluster <- as.integer(args[4]) } else { - quit(save = "no", status = 13, runLast = FALSE) + quit(save = "no", status = 13, runLast = FALSE) } } xgrid <- 10 -if (!args[5] == ""){ - if (!is.na(as.integer(args[5]))){ +if (!args[5] == "") { + if (!is.na(as.integer(args[5]))) { cluster <- as.integer(args[5]) } else { - quit(save = "no", status = 14, runLast = FALSE) + quit(save = "no", status = 14, runLast = FALSE) } } ygrid <- 10 -if (!args[6] == ""){ - if (!is.na(as.integer(args[6]))){ +if (!args[6] == "") { + if (!is.na(as.integer(args[6]))) { cluster <- as.integer(args[6]) } else { - quit(save = "no", status = 14, runLast = FALSE) + quit(save = "no", status = 14, runLast = FALSE) } } seed <- 42 -if (!args[7]==""){ - if (!is.na(as.integer(args[7]))){ +if (!args[7] == "") { + if (!is.na(as.integer(args[7]))) { seed <- as.integer(args[7]) } else { - quit(save = "no", status = 15, runLast = FALSE) + quit(save = "no", status = 15, runLast = FALSE) } } @@ -193,58 +203,59 @@ nodesize <- FALSE nb_args <- length(args) -if (nb_args==16) { +if (nb_args == 16) { plot <- args[8] - if (args[9]=='PDF') { + if (args[9] == "PDF") { plot_pdf <- TRUE } nodesize <- args[10] mplot <- args[11] table <- args[13] mtable <- args[14] - if (args[12]=='meta'){ - flag_meta<-TRUE + if (args[12] == "meta") { + flag_meta <- TRUE } -} else if (nb_args==15){ +} else if (nb_args == 15) { plot <- args[8] - if (args[9]=='PDF') { + if (args[9] == "PDF") { plot_pdf <- TRUE } nodesize <- args[10] table <- args[12] mtable <- args[13] - if (args[11]=='meta'){ - flag_meta<-TRUE + if (args[11] == "meta") { + flag_meta <- TRUE } -} else if (nb_args==13) { +} else if (nb_args == 13) { mplot <- args[8] table <- args[10] mtable <- args[11] - if (args[9]=='meta'){ - flag_meta<-TRUE + if (args[9] == "meta") { + flag_meta <- TRUE } -} else if (nb_args==12) { +} else if (nb_args == 12) { table <- args[9] mtable <- args[10] - if (args[8]=='meta'){ - flag_meta<-TRUE + if (args[8] == "meta") { + flag_meta <- TRUE } -} else if (nb_args==11) { +} else if (nb_args == 11) { plot <- args[8] - if (args[9]=='PDF') { + if (args[9] == "PDF") { plot_pdf <- TRUE } nodesize <- args[10] mplot <- args[11] -} else if (nb_args==10) { +} else if (nb_args == 10) { plot <- args[8] - if (args[9]=='PDF') { + if (args[9] == "PDF") { plot_pdf <- TRUE } nodesize <- args[10] -} else if (nb_args==8){ +} else if (nb_args == 8) { mplot <- args[8] } -flowFrameOrFCS(args[1], args[2], columns, cluster, xgrid, ygrid, plot, plot_pdf, - mplot, flag_default, table, mtable, flag_meta, seed, nodesize) +flow_frame_or_fcs(args[1], args[2], + columns, cluster, xgrid, ygrid, plot, plot_pdf, + mplot, flag_default, table, mtable, flag_meta, seed, nodesize)
--- a/FlowSOMGenerateTree.xml Mon Jul 06 19:50:37 2020 -0400 +++ b/FlowSOMGenerateTree.xml Fri Sep 29 07:20:10 2023 +0000 @@ -1,7 +1,8 @@ -<tool id="flowsom_tree" name="Generate a reference Self Organizing Map" version="1.0+galaxy1" profile="18.01"> +<tool id="flowsom_tree" name="Generate a reference Self Organizing Map" version="1.0+galaxy2" profile="18.01"> <description>using FlowSOM.</description> <requirements> <requirement type="package" version="1.18.0">bioconductor-flowsom</requirement> + <requirement type="package" version="0.0.1">mscorefonts</requirement> </requirements> <stdio> <exit_code range="1:9" level="fatal" description="See stderr for more details." />