# HG changeset patch # User artbio # Date 1618221324 0 # Node ID fec313f5c8894dfef0512ee34ae07202ca3da840 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1" diff -r 000000000000 -r fec313f5c889 pathifier.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pathifier.R Mon Apr 12 09:55:24 2021 +0000 @@ -0,0 +1,311 @@ +################################################################################################## +# Running PATHIFIER (Drier et al., 2013) +# Based on the work of Author: Miguel Angel Garcia-Campos - Github: https://github.com/AngelCampos +################################################################################################## + + +options(show.error.messages = F, error = function() { + cat(geterrmessage(), file = stderr()); q("no", 1, F) + } +) +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +library(pathifier) +library(optparse) +library(pheatmap) +library(scatterplot3d) +library(circlize) + +option_list <- list( + make_option( + "--exp", + type = "character", + help = "Expression matrix"), + make_option( + "--sep", + type = "character", + default = "\t", + help = "File separator [default : '%default']" + ), + make_option( + "--genes", + type = "character", + help = "Gene sets Pathways : gmt format (one pathway per line : Name, description, genes (one by column), tab separated)"), + make_option( + "--is_normal", + default = F, + type = "logical", + help = "Define normals cells in your data"), + make_option( + "--normals", + type = "character", + help = "A vector of sample status : 1 = Healthy, 0 = Tumor. Must be in the same order as in expression data"), + make_option( + "--logfile", + type = "character", + default = "log.txt", + help = "Log file name [default : '%default']" + ), + make_option( + "--max_stability", + type = "logical", + default = T, + help = "If true, throw away components leading to low stability of sampling noise [default : '%default']" + ), + make_option( + "--attempts", + type = "integer", + default = 10, + help = "Number of runs to determine stability. [default : '%default']" + ), + make_option( + "--min_std", + type = "character", + default = "0.4", + help = "Minimum of standard deviation to filter out low variable genes. + Use --min.std data, to use the minimum std of your data [default : '%default']" + ), + make_option( + "--min_exp", + type = "character", + default = "4", + help = "Minimum of gene expression to filter out low expressed genes. + Use --min.exp data, to use the minimum expression of your data [default : '%default']" + ), + make_option( + "--pds", + type = "character", + default = "PDS.tsv", + help = "Output PDS (Pathway deregulation score) of Pathifier in tabular file [default : '%default']" + ), + make_option( + "--heatmap_cluster_cells", + type = "logical", + default = TRUE, + help = "Cluster columns (cells) in the heatmap [default : '%default']" + ), + make_option( + "--heatmap_cluster_pathways", + type = "logical", + default = TRUE, + help = "Cluster rows (pathways) in the heatmap [default : '%default']" + ), + make_option( + "--heatmap_show_cell_labels", + type = "logical", + default = FALSE, + help = "Print column names (cells) on the heatmap [default : '%default']" + ), + make_option( + "--heatmap_show_pathway_labels", + type = "logical", + default = FALSE, + help = "Print row names (pathways) on the heatmap [default : '%default']" + ), + make_option( + "--plot", + type = "character", + default = "./plot.pdf", + help = "Pathifier visualization [default : '%default']" + ), + make_option( + "--rdata", + type = "character", + default = "./results.rdata", + help = "Pathifier object (S4) [default : '%default']")) +parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) +args <- parse_args(parser) +if (args$sep == "tab") { + args$sep <- "\t" +} + + +# set seed for reproducibility +set.seed(123) + +# Load expression data for PATHIFIER +exp_matrix <- as.matrix(read.delim(file = args$exp, + as.is = T, + row.names = 1, + sep = args$sep, + check.names = F)) + +# Load Genesets annotation +gene_sets_file <- file(args$genes, open = "r") +gene_sets <- readLines(gene_sets_file) +close(gene_sets_file) + +# Generate a list that contains genes in genesets +gs <- strsplit(gene_sets, "\t") +names(gs) <- lapply(gs, function(x) x[1]) +gs <- lapply(gs, function(x) x[-c(1:2)]) + +# Generate a list that contains the names of the genesets used +pathwaynames <- names(gs) + +# Prepare data and parameters ################################################## +# Extract information from binary phenotypes. 1 = Normal, 0 = Tumor +if (args$is_normal == T) { + normals <- read.delim(file = args$normals, h = F) + normals <- as.logical(normals[, 2]) + n_exp_matrix <- exp_matrix[, normals] +} else n_exp_matrix <- exp_matrix + +# Calculate MIN_STD +rsd <- apply(n_exp_matrix, 1, sd) +min_std <- quantile(rsd, 0.25) + +# Calculate MIN_EXP +min_exp <- quantile(as.vector(as.matrix(exp_matrix)), + 0.1) # Percentile 10 of data + +# Filter low value genes. At least 10% of samples with values over min_exp +# Set expression levels < MIN_EXP to MIN_EXP +over <- apply(exp_matrix, 1, function(x) x > min_exp) +g_over <- apply(over, 2, mean) +g_over <- names(g_over)[g_over > 0.1] +exp_matrix_filtered <- exp_matrix[g_over, ] +exp_matrix_filtered[exp_matrix_filtered < min_exp] <- min_exp + +# Set maximum 5000 genes with more variance +variable_genes <- names(sort(apply(exp_matrix_filtered, 1, var), decreasing = T))[1:5000] +variable_genes <- variable_genes[!is.na(variable_genes)] +exp_matrix_filtered <- exp_matrix_filtered[variable_genes, ] +allgenes <- as.vector(rownames(exp_matrix_filtered)) + + +if (args$min_std == "data") { + args$min_std <- min_std +} else args$min_std <- as.numeric(args$min_std) + +if (args$min_exp == "data") { + args$min_exp <- min_exp +} else args$min_exp <- as.numeric(args$min_exp) + + +# Open pdf +pdf(args$plot) + +# Construct continuous color scale +col_score_fun <- colorRamp2(c(0, 0.5, 1), c("#4575B4", "#FFFFBF", "#D73027")) + +# Run Pathifier +if (args$is_normal == T) { + pds <- quantify_pathways_deregulation(exp_matrix_filtered, + allgenes, + gs, + pathwaynames, + normals, + maximize_stability = args$max_stability, + attempts = args$attempts, + logfile = args$logfile, + min_std = args$min_std, + min_exp = args$min_exp) + for (i in pathwaynames) { + df <- data.frame(pds$curves[[i]][, 1:3], + normal = normals, + PDS = as.numeric(pds$scores[[i]]), + curve_order = as.vector(pds$curves_order[[i]])) + ordered <- df[df$curve_order, ] + + + layout(cbind(1:2, 1:2), heights = c(7, 1)) + sc3 <- scatterplot3d(ordered[, 1:3], + main = paste("Principal curve of", i), + box = F, pch = 19, type = "l") + sc3$points3d(ordered[, 1:3], box = F, pch = 19, + col = col_score_fun(ordered$PDS)) + + # Plot color scale legend + par(mar = c(5, 3, 0, 3)) + plot(seq(min(ordered$PDS), max(ordered$PDS), length = 100), rep(0, 100), pch = 15, + axes = TRUE, yaxt = "n", xlab = "Color scale of PDS", ylab = "", bty = "n", + col = col_score_fun(seq(min(ordered$PDS), max(ordered$PDS), length = 100))) + + + cols_status <- ifelse(ordered$normal, "blue", "red") + sc3 <- scatterplot3d(ordered[, 1:3], + main = paste("Principal curve of", i), + box = F, pch = "", type = "l") + sc3$points3d(ordered[, 1:3], box = F, + pch = ifelse(ordered$normal, 19, 8), + col = ifelse(ordered$normal, "blue", "red")) + legend("topright", pch = c(19, 8), yjust = 0, + legend = c("normal", "cancer"), + col = c("blue", "red"), cex = 1.1) + + ## annotation for heatmap + sample_status <- data.frame(Status = factor(ifelse(df$normal, "normal", "tumor"))) + rownames(sample_status) <- colnames(exp_matrix_filtered) + color_status_heatmap <- list(Status = c(normal = "blue", tumor = "red")) + } +} else{ + pds <- quantify_pathways_deregulation(exp_matrix_filtered, + allgenes, + gs, + pathwaynames, + maximize_stability = args$max_stability, + attempts = args$attempts, + logfile = args$logfile, + min_std = args$min_std, + min_exp = args$min_exp) + for (i in pathwaynames) { + df <- data.frame(pds$curves[[i]][, 1:3], + PDS = as.numeric(pds$scores[[i]]), + curve_order = as.vector(pds$curves_order[[i]])) + ordered <- df[df$curve_order, ] + + layout(cbind(1:2, 1:2), heights = c(7, 1)) + sc3 <- scatterplot3d(ordered[, 1:3], + main = paste("Principal curve of", i), + box = F, pch = 19, type = "l") + sc3$points3d(ordered[, 1:3], box = F, pch = 19, + col = col_score_fun(ordered$PDS)) + + # Plot color scale legend + par(mar = c(5, 3, 0, 3)) + plot(seq(min(ordered$PDS), max(ordered$PDS), length = 100), rep(0, 100), pch = 15, + axes = TRUE, yaxt = "n", xlab = "Color scale of PDS", ylab = "", bty = "n", + col = col_score_fun(seq(min(ordered$PDS), max(ordered$PDS), length = 100))) + + + ## annotation for heatmap (for the moment none for this situation) + sample_status <- NA + color_status_heatmap <- NA + } +} + +## Create dataframe from Pathifier list and round score to 4 digits +pds_scores <- mapply(FUN = function(x) cbind(round(x, 4)), pds$scores) +dimnames(pds_scores) <- list(colnames(exp_matrix_filtered), names(pds$scores)) + +## plot heatmap +if (ncol(pds_scores) > 1) { + pheatmap(t(pds_scores), + main = "Heatmap of Pathway Deregulation Score", # heat map title + cluster_rows = args$heatmap_cluster_pathways, # apply clustering method + cluster_cols = args$heatmap_cluster_cells, # apply clustering method + + #Additional Options + ## Color labeled columns + annotation_col = sample_status, + annotation_colors = color_status_heatmap, + show_rownames = args$heatmap_show_pathway_labels, + show_colnames = args$heatmap_show_cell_labels, + border_color = NA, + legend = TRUE) +} +dev.off() + + +## write table +write.table(pds_scores, + args$pds, + row.names = T, + col.names = T, + quote = F, + sep = "\t") + +## write S4 pathifier object +save(pds, file = args$rdata) diff -r 000000000000 -r fec313f5c889 pathifier.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pathifier.xml Mon Apr 12 09:55:24 2021 +0000 @@ -0,0 +1,192 @@ + + : Quantify deregulation of pathways in cancer + + r-optparse + bioconductor-pathifier + r-pheatmap + r-scatterplot3d + r-circlize + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + log == 'yes' + + + + rds == 'yes' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Pathifier is an algorithm that infers pathway deregulation scores for each (tumor) sample on the basis +of expression data. This score is determined, in a context-specific manner, for every particular dataset +and type of cancer that is being investigated. The algorithm transforms gene-level information into +pathway-level information, generating a compact and biologically relevant representation of each sample. + +For each pathway analysed, the transcriptome datasets are plotted in the gene pathway space using a +Principal Component analysis (PCA) and a principal curve is regressed from these points. All transcriptomes +are projected on the nearest point of this curve. Pathifier finally computes a score which corresponds to +the distance (normalized to 1) of each point (transcriptome) to the curve origin. + +**Inputs** + + * a matrix of n columns of observations (generally RNAseq experiments) and k rows of variables (generally k genes). + * a Gene Matrix Transposed file (GMT format) where each row represents a gene set : + * first column : gene set name (pathway name) + * second : description of gene set + * third and + : list of genes that composed the gene set tab-separated + * (Optional) a two column table with no header, to described transcriptome status (Tumor or not) : + * first column : sample labels + * second : levels of sample status : 1 = Healthy, 0 = Tumor + +**Outputs** + + * Table of Pathway Deregulation Scores : one by pathway (column) and by transcriptome (row) + * Visualization of PDS (pdf) : + * Principal curve of different PDS + * Heatmap of PDS that allows (through clustering) to see pattern in pathway deregulation + * (Optional) Log file of Pathifier algorithm + * (Optional) Pathifier S4 object which contains all informations and results generated by Pathifier, for each pathway : + * `scores` : PDS scores + * `genesinpathway` : Gene identifiers in each pathway + * `newmeanstd` + * `origmeanstd` + * `pathwaysize` : Number of genes retained in pathway + * `curves` : Coordinates of transcriptomes projected on the principal curve + * `curves_order` : Order of transcriptomes along the principal curve + * `z` : z-scores matrix + * `compin` + * `xm` + * `xs` + * `center` + * `rot` + * `pctaken` : Number of principal component retained for pathifier analysis + * `samplings` + * `sucess` : List of pathway index that passed Pathfiier filters (more info in log file) + * `logfile` : Name of logfile + + + + @Manual{, + title = {{pathifier}: Quantify deregulation of pathways in cancer}, + author = {Yotam Drier}, + year = {2013-06-27}, + note = {R package version 1.22.0}, + url = {https://git.bioconductor.org/packages/pathifier}, + } + + @article {Drier6388, + author = {Drier, Yotam and Sheffer, Michal and Domany, Eytan}, + title = {Pathway-based personalized analysis of cancer}, + volume = {110}, + number = {16}, + pages = {6388--6393}, + year = {2013}, + doi = {10.1073/pnas.1219651110}, + publisher = {National Academy of Sciences}, + issn = {0027-8424}, + URL = {https://www.pnas.org/content/110/16/6388}, + eprint = {https://www.pnas.org/content/110/16/6388.full.pdf}, + journal = {Proceedings of the National Academy of Sciences} + } + + + diff -r 000000000000 -r fec313f5c889 test-data/kegg_pathways.gmt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kegg_pathways.gmt Mon Apr 12 09:55:24 2021 +0000 @@ -0,0 +1,2 @@ +MISMATCH_REPAIR NA EXO1 LIG1 MLH1 MLH3 MSH2 MSH3 MSH6 PCNA PMS2 POLD1 POLD2 POLD3 POLD4 RFC1 RFC2 RFC3 RFC4 RFC5 RPA1 RPA2 RPA3 RPA4 SSBP1 +REGULATION_OF_AUTOPHAGY NA ATG12 ATG3 ATG4A ATG4B ATG4C ATG4D ATG5 ATG7 BECN1 BECN1L1 GABARAP 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