Mercurial > repos > ppericard > viscorvar
diff mixomics_blocksplsda_script.R @ 0:d0b77b926863 draft
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
author | ppericard |
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date | Tue, 23 Jun 2020 19:57:35 -0400 |
parents | |
children | e93350dc99f1 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_blocksplsda_script.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,233 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +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") + +## Get parameters ## +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Run the mixOmics block.splsda function') + +parser$add_argument('--block', dest='blocks_list', nargs=4, action="append", required=TRUE, + help="Block name + nb variables to select + data matrix file + variables metadata file") +parser$add_argument('--sample_metadata_in', dest='sample_metadata_in', required=TRUE, + help="Samples metadata file") +parser$add_argument('--sample_description_col', dest='sample_description_col', type='integer', + default=0, help="Sample description column number") +parser$add_argument('--ncomp', dest='ncomp', type='integer', default=2, + help="Number of components to include in the model") +parser$add_argument('--correlation', dest='correlation', action="store_true", + help="Add correlation between all blocks") +parser$add_argument('--scheme', dest='scheme', default="horst", help="Scheme") +parser$add_argument('--mode', dest='mode', default="regression", help="Mode") +parser$add_argument('--maxiter', dest='maxiter', type='integer', default=100, + help="Maximum number of iterations") +parser$add_argument('--scale', dest='scale', action="store_true", + help="Each block is standardized to zero means and unit variances") +parser$add_argument('--check_missing_values', dest='check_missing_values', action="store_true", + help="Check for missing values and raise an error") +parser$add_argument('--init', dest='init', default="svd", + help="Init (svd or svd.single)") +parser$add_argument('--tol', dest='tol', type='double', default=1e-06, + help="Convergence stopping value") +parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true", + help="Should be set in particular for data with many zero values") +parser$add_argument('--rdata_out', dest='rdata_out', required=TRUE, help="Output Rdata file") +parser$add_argument('--sample_metadata_out', dest='sample_metadata_out', required=TRUE, help="Output sample metadata file") +parser$add_argument('--variable_metadata_outdir', dest='variable_metadata_outdir', required=TRUE, help="Output variable metadata directory") + +args <- parser$parse_args() + +## Print parameters +print("Blocks:") +print(args$blocks_list) +print("Sample metadata file:") +print(args$sample_metadata_in) +print("Sample description column number:") +print(args$sample_description_col) +print("Number of components:") +print(args$ncomp) +print("Compute correlation between all blocks:") +print(args$correlation) +print("Scheme:") +print(args$scheme) +print("Mode:") +print(args$mode) +print("Max nb of iterations:") +print(args$maxiter) +print("Scale:") +print(args$scale) +print("Check for missing values:") +print(args$check_missing_values) +print("Tol:") +print(args$tol) +print("near.zero.var:") +print(args$nearzerovar) +print("Output Rdata file:") +print(args$rdata_out) +print("Output sample metadata file:") +print(args$sample_metadata_out) +print("Output variable metadata directory:") +print(args$variable_metadata_outdir) + +## Loading libraries +suppressPackageStartupMessages(require(mixOmics)) + +## Read sample metadata file and set description factor matrix +sample_metadata <- read.table(args$sample_metadata_in, sep='\t', header=TRUE, row.names=1) +sample_metadata_names <- row.names(sample_metadata) +# print(sample_metadata_names) + +# print("Sample metadata matrix:") +# print(head(sample_metadata)) + +description_column <- ncol(sample_metadata) +if(args$sample_description_col > 0) +{ + description_column <- args$sample_description_col +} + +Y <- factor(sample_metadata[[description_column]]) + +print("Y factor matrix:") +print(Y) + +## Read and prepare block datasets +list_X <- c() +keepX <- c() + +for(i in 1:nrow(args$blocks_list)) +{ + # Read block input parameters + block_name <- args$blocks_list[i,1] + block_keep <- strtoi(args$blocks_list[i,2]) + block_data_matrix_filename <- args$blocks_list[i,3] + # block_meta_var <- args$blocks_list[i,4] + + print(sprintf("Processing block %s", block_name)) + + # Store block data matrices + block_data_matrix <- t(read.table(block_data_matrix_filename, sep='\t', header=TRUE, row.names=1)) # transpose the matrix so that the samples become rows and the variables become columns + block_data_matrix_names <- row.names(block_data_matrix) + # print(block_data_matrix_names) + + if(!identical(sample_metadata_names, block_data_matrix_names)) + { + stop("Sample names must be the same and in the same order in the sample metadata matrix and the block data matrix") + } + + list_X[[block_name]] <- block_data_matrix + + # Set the nb of variables to keep + nb_variables = ncol(list_X[[block_name]]) + if(block_keep > 0) + { + keepX[[block_name]] <- rep(block_keep, args$ncomp) + } + else + { + keepX[[block_name]] <- rep(nb_variables, args$ncomp) + } + print(sprintf("Block %s contains %d variables and %d will be selected", block_name, nb_variables, block_keep)) +} + +# print(list_X) + +## Generate design matrix +block_nb <- nrow(args$blocks_list) + +design <- matrix(0, nrow = block_nb, ncol = block_nb) + +if(args$correlation) +{ + design <- matrix(1, nrow = block_nb, ncol = block_nb) + diag(design) <- 0 +} + +# print("Design matrix:") +# print(design) + +################### +## Main function ## +################### + +mixomics_result <- block.splsda(X = list_X, + Y = Y, + ncomp = args$ncomp, + keepX = keepX, + design = design, + scheme = args$scheme, + mode = args$mode, + scale = args$scale, + init = args$init, + tol = args$tol, + max.iter = args$maxiter, + near.zero.var = args$nearzerovar, + all.outputs = TRUE) + +print("Block.splsda object:") +print(mixomics_result) +print(attributes(mixomics_result)) + +## Save output Rdata file +save(mixomics_result, file=args$rdata_out) + +## Save output sample metadata file +# print("Block.splsda variates:") +# print(mixomics_result$variates) + +for(block_name in names(mixomics_result$variates)) +{ + # print(block_name) + # print(mixomics_result$variates[[block_name]]) + + # Format the column names to add the block name and replace spaces + colnames(mixomics_result$variates[[block_name]]) <- paste("block.splsda_variates", block_name, gsub(" ", "_", colnames(mixomics_result$variates[[block_name]])), sep = "_") + # print(mixomics_result$variates[[block_name]]) + + # Append the new columns to the sample metadata matrix + sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[block_name]]) +} + +# print(sample_metadata) + +write.table(sample_metadata, file = args$sample_metadata_out, quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA) + +## Save output variable metadata files in output directory +# print("Block.splsda loadings:") +# print(mixomics_result$loadings) + +for(i in 1:nrow(args$blocks_list)) +{ + # Read again block input parameters + block_name <- args$blocks_list[i,1] + # block_keep <- strtoi(args$blocks_list[i,2]) + # block_data_matrix_filename <- args$blocks_list[i,3] + block_meta_var <- args$blocks_list[i,4] + + print(sprintf("Saving block %s output metavar", block_name)) + + meta_variable <- mixomics_result$loadings[[block_name]] + # print(head(meta_variable)) + + # Format the column names to add the block name and replace spaces + colnames(meta_variable) <- paste("block.splsda_loadings", gsub(" ", "_", colnames(meta_variable)), sep = "_") + + # Read input block variable metadata files if provided (optional) + if(block_meta_var != "None") + { + input_meta_variable <- read.table(block_meta_var, sep='\t', header=TRUE, row.names=1) + # print(head(input_meta_variable)) + + # Append the new columns to the variable metadata matrix + meta_variable <- cbind2(input_meta_variable, meta_variable) + } + + # print(head(meta_variable)) + + block_meta_var_output_filename <- paste("mixomics_blocksplsda_block_", block_name, "_variable_metadata.tsv", sep="") + write.table(meta_variable, file = paste(args$variable_metadata_outdir,block_meta_var_output_filename, sep='/'), quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA) +} \ No newline at end of file