# HG changeset patch # User azomics # Date 1695971982 0 # Node ID 33b8673272cfe529cf91a82ff31611d2dc18b06e # Parent bd35f3b66a1e8d78dcc593210ad3b73ebbe81ff3 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d diff -r bd35f3b66a1e -r 33b8673272cf FlowSOMCompare.R --- a/FlowSOMCompare.R Mon Jun 22 17:54:03 2020 -0400 +++ b/FlowSOMCompare.R Fri Sep 29 07:19:42 2023 +0000 @@ -1,4 +1,4 @@ -#!/usr/bin/Rscript +#!/usr/bin/env Rscript # Module for Galaxy # Compares groups of FCS to FlowSOM reference tree # with FlowSOM @@ -14,181 +14,208 @@ library(FlowSOM) library(flowCore) -checkFiles <- function(groups){ +check_files <- function(groups) { all_files <- unlist(groups) all_unique <- unique(all_files) if (length(all_unique) != length(all_files)) { - quit(save = "no", status = 14, runLast = FALSE) + quit(save = "no", status = 14, runLast = FALSE) } } -compareLists <- function(m1, m2){ - listCheck <- T - if (is.na(all(m1==m2))) { +compare_lists <- function(m1, m2) { + list_check <- TRUE + if (is.na(all(m1 == m2))) { mm1 <- is.na(m1) mm2 <- is.na(m2) - if (all(mm1==mm2)){ - if (!all(m1==m2, na.rm=TRUE)){ - listCheck <- F + if (all(mm1 == mm2)) { + if (!all(m1 == m2, na.rm = TRUE)) { + list_check <- FALSE } } else { - listCheck <- F + list_check <- FALSE } - } else if (!all(m1==m2)) { - listCheck <- F + } else if (!all(m1 == m2)) { + list_check <- FALSE } - return(listCheck) + return(list_check) } -prettyMarkerNames <- function(flowFrame){ - n <- flowFrame@parameters@data[, "name"] - d <- flowFrame@parameters@data[, "desc"] +pretty_marker_names <- function(flow_frame) { + n <- flow_frame@parameters@data[, "name"] + d <- flow_frame@parameters@data[, "desc"] d[is.na(d)] <- n[is.na(d)] - prettyNames <- list() - if(any(grepl("#",d))){ - # Support for hashtag notation: - # antibody#fluorochrome -> antibody (fluorochrome) - prettyNames <- gsub("#(.*)$"," (\\1)",d) + pretty_names <- list() + if (any(grepl("#", d))) { + # Support for hashtag notation: + pretty_names <- gsub("#(.*)$", " (\\1)", d) } else { - prettyNames <- paste(d, " <", n, ">", sep="") + pretty_names <- paste(d, " <", n, ">", sep = "") } - return(prettyNames) + return(pretty_names) } -compareToTree <- function(fst, wilc_thresh=0.05, output="", plot="", stats, - comp_groups, filenames) { - groupRes <- CountGroups(fst, groups=comp_groups, plot=FALSE) - pdf(plot, useDingbats=FALSE, onefile=TRUE) +compare_to_tree <- function(fst, + wilc_thresh = 0.05, output = "", plot = "", stats, + comp_groups, filenames) { + group_res <- CountGroups(fst, groups = comp_groups, plot = FALSE) + pdf(plot, useDingbats = FALSE, onefile = TRUE) tresh <- wilc_thresh - pg <- PlotGroups(fst, groupRes, p_tresh=tresh) + pg <- PlotGroups(fst, group_res, p_tresh = tresh) dev.off() nb_nodes <- length(pg[[1]]) nb_comp <- length(pg) - m <- matrix(0, nrow=nb_nodes, ncol=nb_comp+1) + m <- matrix(0, nrow = nb_nodes, ncol = nb_comp + 1) s <- seq_len(nb_nodes) - m[,1]<- as.character(s) - for (i in 1:nb_comp){ - m[s,i+1]<- as.character(pg[[i]]) + m[, 1] <- as.character(s) + for (i in 1:nb_comp) { + m[s, i + 1] <- as.character(pg[[i]]) } - groupnames <- attr(comp_groups,"names") - out_colnames <- paste(groupnames, collapse="-") - colnames(m) <- c("Node",out_colnames) - write.table(m, file=output, quote=F, row.names=F, col.names=T, sep='\t', - append=F) + groupnames <- attr(comp_groups, "names") + out_colnames <- paste(groupnames, collapse = "-") + colnames(m) <- c("Node", out_colnames) + write.table(m, file = output, quote = FALSE, row.names = FALSE, + col.names = TRUE, sep = "\t", + append = FALSE) ## get filenames filepaths <- unlist(comp_groups) fnames <- unlist(filenames) nb_files <- length(filepaths) comp_files <- list() - for (i in 1:length(filepaths)){ + for (i in seq_along(filepaths)) { comp_files[[filepaths[[i]]]] <- fnames[[i]] } group_list <- list() for (grp in attr(comp_groups, "names")) { - for (f in comp_groups[[grp]]){ + for (f in comp_groups[[grp]]) { group_list[[f]] <- grp } } out_stats <- attr(stats, "names") - if ("counts" %in% out_stats){ - gp_counts <- as.matrix(groupRes$counts) - tpc <- matrix("", nrow=nb_files, ncol=2) - tpc[,1] <- as.character(lapply(rownames(gp_counts), function(x) comp_files[[x]])) - tpc[,2] <- as.character(lapply(rownames(gp_counts), function(x) group_list[[x]])) + if ("counts" %in% out_stats) { + gp_counts <- as.matrix(group_res$counts) + tpc <- matrix("", nrow = nb_files, ncol = 2) + tpc[, 1] <- as.character( + lapply(rownames(gp_counts), + function(x) comp_files[[x]])) + tpc[, 2] <- as.character( + lapply(rownames(gp_counts), + function(x) group_list[[x]])) gp_counts <- cbind(tpc, gp_counts) colnames(gp_counts)[[1]] <- "Filename" colnames(gp_counts)[[2]] <- "Group" t_gp_counts <- t(gp_counts) - write.table(t_gp_counts, file=stats[["counts"]], quote=F, row.names=T, col.names=F, sep='\t', - append=F) + write.table(t_gp_counts, + file = stats[["counts"]], + quote = FALSE, + row.names = TRUE, + col.names = FALSE, + sep = "\t", + append = FALSE) } - if ("pctgs" %in% out_stats){ - gp_prop <- as.matrix(groupRes$pctgs) - tpp <- matrix("", nrow=nb_files, ncol=2) - tpp[,1] <- as.character(lapply(rownames(gp_prop), function(x) comp_files[[x]])) - tpp[,2] <- as.character(lapply(rownames(gp_prop), function(x) group_list[[x]])) + if ("pctgs" %in% out_stats) { + gp_prop <- as.matrix(group_res$pctgs) + tpp <- matrix("", nrow = nb_files, ncol = 2) + tpp[, 1] <- as.character( + lapply(rownames(gp_prop), + function(x) comp_files[[x]])) + tpp[, 2] <- as.character( + lapply(rownames(gp_prop), + function(x) group_list[[x]])) gp_prop <- cbind(tpp, gp_prop) colnames(gp_prop)[[1]] <- "Filename" colnames(gp_prop)[[2]] <- "Group" t_gp_prop <- t(gp_prop) - write.table(t_gp_prop, file=stats[["pctgs"]], quote=F, row.names=T, col.names=F, sep='\t', - append=F) + write.table(t_gp_prop, + file = stats[["pctgs"]], + quote = FALSE, + row.names = TRUE, + col.names = FALSE, + sep = "\t", + append = FALSE) } - if ("means" %in% out_stats){ - gp_mean <- as.matrix(groupRes$means) + if ("means" %in% out_stats) { + gp_mean <- as.matrix(group_res$means) t_gp_mean <- t(gp_mean) - tpm <- matrix(0, nrow=nb_nodes, ncol=1) - tpm[,1] <- seq_len(nb_nodes) + tpm <- matrix(0, nrow = nb_nodes, ncol = 1) + tpm[, 1] <- seq_len(nb_nodes) t_gp_mean <- cbind(tpm, t_gp_mean) colnames(t_gp_mean)[[1]] <- "Nodes" - write.table(t_gp_mean, file=stats[["means"]], quote=F, row.names=F, col.names=T, sep='\t', - append=F) + write.table(t_gp_mean, + file = stats[["means"]], + quote = FALSE, + row.names = FALSE, + col.names = TRUE, + sep = "\t", + append = FALSE) } - if ("medians" %in% out_stats){ - gp_med <- as.matrix(groupRes$medians) + if ("medians" %in% out_stats) { + gp_med <- as.matrix(group_res$medians) t_gp_med <- t(gp_med) - tpd <- matrix(0, nrow=nb_nodes, ncol=1) - tpd[,1] <- seq_len(nb_nodes) + tpd <- matrix(0, nrow = nb_nodes, ncol = 1) + tpd[, 1] <- seq_len(nb_nodes) t_gp_med <- cbind(tpd, t_gp_med) colnames(t_gp_med)[[1]] <- "Nodes" - write.table(t_gp_med, file=stats[["medians"]], quote=F, row.names=F, col.names=T, sep='\t', - append=F) + write.table(t_gp_med, + file = stats[["medians"]], + quote = FALSE, + row.names = FALSE, + col.names = TRUE, + sep = "\t", + append = FALSE) } } -checkFCS <- function(tree, output="", plot="", thresh = 0.05, stats, groups, - filenames) { +check_fcs <- function(tree, + output = "", plot = "", thresh = 0.05, stats, groups, + filenames) { fcsfiles <- unlist(groups) - tree_valid <- F - markerCheck <- T + tree_valid <- FALSE + marker_check <- TRUE tryCatch({ fsomtree <- readRDS(tree) - tree_valid <- T + tree_valid <- TRUE }, error = function(ex) { print(paste(ex)) }) - fst <- if (length(fsomtree)==2) fsomtree[[1]] else fsomtree + fst <- if (length(fsomtree) == 2) fsomtree[[1]] else fsomtree - if (tree_valid){ + if (tree_valid) { tree_markers <- as.vector(fst$prettyColnames) - tree_channels <- as.vector(colnames(fst$data)) - if (length(tree_markers) < 1){ + if (length(tree_markers) < 1) { quit(save = "no", status = 11, runLast = FALSE) } } else { quit(save = "no", status = 11, runLast = FALSE) } - for (i in 1:length(fcsfiles)){ - is_file_valid <- F + for (i in seq_along(fcsfiles)) { tryCatch({ - fcs <- read.FCS(fcsfiles[i], transformation=FALSE) - is_file_valid <- T + fcs <- read.FCS(fcsfiles[i], transformation = FALSE) }, error = function(ex) { print(paste(ex)) }) - if (i == 1) { + if (i == 1) { m1 <- as.vector(pData(parameters(fcs))$desc) c1 <- colnames(fcs) # compare to tree markers - pm <- prettyMarkerNames(fcs) - if (!all(tree_markers %in% pm)){ + pm <- pretty_marker_names(fcs) + if (!all(tree_markers %in% pm)) { quit(save = "no", status = 13, runLast = FALSE) } } else { m2 <- as.vector(pData(parameters(fcs))$desc) c2 <- colnames(fcs) - markerCheck <- compareLists(m1,m2) - markerChannel <- compareLists(c1,c2) + marker_check <- compare_lists(m1, m2) + marker_channel <- compare_lists(c1, c2) } } - if (markerCheck && markerChannel) { - compareToTree(fst, thresh, output, plot, stats, groups, filenames) + if (marker_check && marker_channel) { + compare_to_tree(fst, thresh, output, plot, stats, groups, filenames) } else { quit(save = "no", status = 12, runLast = FALSE) } @@ -201,28 +228,28 @@ g <- list() tmplist <- c("counts", "means", "medians", "pctgs") -for (i in 5:13){ - if (args[i] %in% tmplist){ +for (i in 5:13) { + if (args[i] %in% tmplist) { first_g1 <- first_g1 + 2 - g[[args[i]]] <- args[i+1] + g[[args[i]]] <- args[i + 1] } } -tmpargs <- paste(args[first_g1:tot_args], collapse="=%=") +tmpargs <- paste(args[first_g1:tot_args], collapse = "=%=") tmpgroups <- strsplit(tmpargs, "=%=DONE=%=") groups <- list() filenames <- list() for (gps in tmpgroups[[1]]) { tmpgroup <- strsplit(gps, "=%=") - nb_files <- (length(tmpgroup[[1]]) - 1 ) /2 + nb_files <- (length(tmpgroup[[1]]) - 1) / 2 tmplist <- character(nb_files) tmpnames <- character(nb_files) j <- 1 - for (i in 2:length(tmpgroup[[1]])){ - if (!i%%2){ + for (i in 2:length(tmpgroup[[1]])) { + if (!i %% 2) { tmplist[[j]] <- tmpgroup[[1]][i] - tmpnames[[j]]<- tmpgroup[[1]][i+1] + tmpnames[[j]] <- tmpgroup[[1]][i + 1] j <- j + 1 } } @@ -230,5 +257,5 @@ filenames[[tmpgroup[[1]][1]]] <- tmpnames } -checkFiles(groups) -checkFCS(args[1], args[2], args[3], args[4], g, groups, filenames) +check_files(groups) +check_fcs(args[1], args[2], args[3], args[4], g, groups, filenames) diff -r bd35f3b66a1e -r 33b8673272cf FlowSOMCompare.xml --- a/FlowSOMCompare.xml Mon Jun 22 17:54:03 2020 -0400 +++ b/FlowSOMCompare.xml Fri Sep 29 07:19:42 2023 +0000 @@ -1,7 +1,8 @@ - + using a FlowSOM tree bioconductor-flowsom + mscorefonts