diff mixomics_blocksplsda_script.R @ 0:bea08702ed51 draft

planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a

--- /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)
+}
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