# HG changeset patch # User ppericard # Date 1558083622 14400 # Node ID bea08702ed51839f438cdc08a59a604a84894fd6 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a diff -r 000000000000 -r bea08702ed51 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Fri May 17 05:00:22 2019 -0400 @@ -0,0 +1,661 @@ + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +. diff -r 000000000000 -r bea08702ed51 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri May 17 05:00:22 2019 -0400 @@ -0,0 +1,2 @@ +# galaxy-mixomics-blocksplsda +Galaxy wrappers for the block.splsda, plotIndiv and plotVar functions from the mixOmics R package diff -r 000000000000 -r bea08702ed51 mixomics_blocksplsda.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_blocksplsda.xml Fri May 17 05:00:22 2019 -0400 @@ -0,0 +1,224 @@ + + + performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis + + + bioconductor-mixomics + r-argparse + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1371/journal.pcbi.1005752 + + + \ No newline at end of file diff -r 000000000000 -r bea08702ed51 mixomics_blocksplsda_script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_blocksplsda_script.R Fri May 17 05:00:22 2019 -0400 @@ -0,0 +1,213 @@ +#!/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$add_argument('--sample_description_col', dest='sample_description_col', type='integer', required=TRUE, help="Sample description column number") +parser$add_argument('--ncomp', dest='ncomp', type='integer', required=TRUE, 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', required=TRUE, help="Scheme") +parser$add_argument('--mode', dest='mode', required=TRUE, help="Mode") +parser$add_argument('--maxiter', dest='maxiter', type='integer', required=TRUE, 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('--init', dest='init', required=TRUE, help="Init (svd or svd.single)") +parser$add_argument('--tol', dest='tol', type='double', required=TRUE, help="Convergence stopping value") +parser$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$scale) +print("Tol:") +print(args$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) + +## 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(bname in names(mixomics_result$variates)) +{ + # print(bname) + # print(mixomics_result$variates[[bname]]) + + # Format the column names to add the block name and replace spaces + colnames(mixomics_result$variates[[bname]]) <- paste("block.splsda", bname, gsub(" ", "_", colnames(mixomics_result$variates[[bname]])), sep = "_") + # print(mixomics_result$variates[[bname]]) + + # Append the new columns to the sample metadata matrix + sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[bname]]) +} + +# 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$blocks_list[i,4] + + meta_variable <- mixomics_result$loadings[[block_name]] + # print(head(meta_variable)) + + # 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$variable_metadata_outdir,block_meta_var_output_filename, sep='/'), quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA) +} \ No newline at end of file diff -r 000000000000 -r bea08702ed51 mixomics_plotindiv.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_plotindiv.xml Fri May 17 05:00:22 2019 -0400 @@ -0,0 +1,107 @@ + + + provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA) + + + bioconductor-mixomics + r-argparse + + + + + + + + + + + + +
+ + +
+ + + + + + + + + + + + + + + + + + + 10.1371/journal.pcbi.1005752 + + + \ No newline at end of file diff -r 000000000000 -r bea08702ed51 mixomics_plotindiv_script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_plotindiv_script.R Fri May 17 05:00:22 2019 -0400 @@ -0,0 +1,53 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Main Function ## + +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Run the mixOmics plotIndiv function') + +parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") +parser$add_argument('--legend', dest='legend', action="store_true", help="Display the legend") +parser$add_argument('--ellipse', dest='ellipse', action="store_true", help="Plot ellipse plots") +parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file") + +args <- parser$parse_args() + +## +print("Input RData:") +print(args$input_rdata) +print("Plot legend:") +print(args$legend) +print("Plot ellipse plots:") +print(args$ellipse) +print("Output PDF file:") +print(args$output_pdf) + +# loading libraries +suppressPackageStartupMessages(require(mixOmics)) + +load(args$input_rdata) + +pdf(args$output_pdf) + +plotIndiv(mixomics_result, + legend = args$legend, + ellipse = args$ellipse) + +for(k in 1:(length(mixomics_result$names[[3]])-1)) +{ + name_block = mixomics_result$names[[3]][k] + + plotIndiv(mixomics_result, + blocks = k, + legend = args$legend, + ellipse = args$ellipse) +} + +dev.off() \ No newline at end of file diff -r 000000000000 -r bea08702ed51 mixomics_plotvar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_plotvar.xml Fri May 17 05:00:22 2019 -0400 @@ -0,0 +1,107 @@ + + + provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA + + + bioconductor-mixomics + r-argparse + + + + + + + + + + + + +
+ + +
+ + + + + + + + + + + + + + + + + + + 10.1371/journal.pcbi.1005752 + + + \ No newline at end of file diff -r 000000000000 -r bea08702ed51 mixomics_plotvar_script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_plotvar_script.R Fri May 17 05:00:22 2019 -0400 @@ -0,0 +1,53 @@ +#!/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") + +## Main Function ## + +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Run the mixOmics plotVar function') + +parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") +parser$add_argument('--legend', dest='legend', action="store_true", help="Display the legend") +parser$add_argument('--cutoff', dest='cutoff', type='double', required=TRUE, help="Cutoff (0..1)") +parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file") + +args <- parser$parse_args() + +## +print("Input RData:") +print(args$input_rdata) +print("Plot legend:") +print(args$legend) +print("Cutoff:") +print(args$cutoff) +print("Output PDF file:") +print(args$output_pdf) + +# loading libraries +suppressPackageStartupMessages(require(mixOmics)) + +load(args$input_rdata) + +pdf(args$output_pdf) + +plotVar(mixomics_result, + legend = args$legend, + cutoff = args$cutoff) + +for(k in 1:(length(mixomics_result$names[[3]])-1)) +{ + name_block = mixomics_result$names[[3]][k] + + plotVar(mixomics_result, + blocks = k, + legend = args$legend, + cutoff = args$cutoff) +} + +dev.off() \ No newline at end of file diff -r 000000000000 -r bea08702ed51 test-data/in_block1_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_block1_data.tabular Fri May 17 05:00:22 2019 -0400 @@ -0,0 +1,7 @@ + "A1" "A2" "B1" "B2" +"var1" 1 2 3 4 +"var2" 1.5 2.5 3.5 4.5 +"var3" 2.5 2 2.5 2 +"var4" 5 4 3 2 +"var5" 1.001 1.01 1.1 1 +"var6" 10 13 11 10 diff -r 000000000000 -r bea08702ed51 test-data/in_block2_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_block2_data.tabular Fri May 17 05:00:22 2019 -0400 @@ -0,0 +1,7 @@ + "A1" "A2" "B1" "B2" +"var1" 2 3 4 5 +"var2" 2.5 1 2.5 4 +"var3" 2.5 2 2.5 2 +"var4" 6 5 3 2 +"var5" 10.001 10.01 10.1 10 +"var6" 20 23 21 20 diff -r 000000000000 -r bea08702ed51 test-data/in_sample_meta.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_sample_meta.tabular Fri May 17 05:00:22 2019 -0400 @@ -0,0 +1,5 @@ + "Y" +"A1" "catA" +"A2" "catA" +"B1" "catB" +"B2" "catB" diff -r 000000000000 -r bea08702ed51 test-data/out_plotIndiv.pdf Binary file test-data/out_plotIndiv.pdf has changed diff -r 000000000000 -r bea08702ed51 test-data/out_plotVar.pdf Binary file test-data/out_plotVar.pdf has changed diff -r 000000000000 -r bea08702ed51 test-data/out_rdata.rdata Binary file test-data/out_rdata.rdata has changed diff -r 000000000000 -r bea08702ed51 test-data/out_sample_meta.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_sample_meta.tabular Fri May 17 05:00:22 2019 -0400 @@ -0,0 +1,5 @@ +"" "Y" "block.splsda_Block1_comp1" "block.splsda_Block1_comp2" "block.splsda_Block2_comp1" "block.splsda_Block2_comp2" "block.splsda_Y_comp1" "block.splsda_Y_comp2" +"A1" "catA" 1.85013467343542 0.422684485040581 1.28016568038406 0.405956759170116 1.22474487139159 0.0342790721507239 +"A2" "catA" 1.07324868851916 -0.960001503242697 1.53872954309497 -0.749531756995324 1.22474487139159 -0.16259622770647 +"B1" "catB" -1.0856729590951 1.64317643604658 -1.01949098398762 1.60513370686125 -1.22474487139159 0.374128476201717 +"B2" "catB" -1.83771040285949 -1.10585941784446 -1.79940423949142 -1.26155870903602 -1.22474487139159 -0.245811320645977