Mercurial > repos > ppericard > mixomics_blocksplsda
diff matCor_addVar_wrapper.R @ 3:0a3c83f2197a draft
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
author | ppericard |
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date | Fri, 25 Oct 2019 07:10:59 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matCor_addVar_wrapper.R Fri Oct 25 07:10:59 2019 -0400 @@ -0,0 +1,93 @@ +#!/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='Compute the matCorEtBlockSelect and addVariablesReponses functions') + +parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") +parser$add_argument('--cutoff_comp', dest='cutoff_comp', type='double', required=TRUE, help="") +parser$add_argument('--mat_block_Y_file', dest='mat_block_Y_file', required=TRUE, help="Matrix block Y filepath") +parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file") +parser$add_argument('--output_blocks_comb', dest='output_blocks_comb', required=TRUE, help="Output blocks combinations file") + +args <- parser$parse_args() + +## Print parameters +print("Input RData:") +print(args$input_rdata) +print("Cutoff comp:") +print(args$cutoff_comp) +print("Mat Block Y file:") +print(args$mat_block_Y_file) +print("Output RData:") +print(args$output_rdata) +print("Output Blocks combinations:") +print(args$output_blocks_comb) + +## Loading libraries +suppressPackageStartupMessages(require(mixOmics)) + +# R script call +source_local <- function(fname) +{ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} +## Loading local functions +source_local("Integration_block_splsda_fonc.R") + +load(args$input_rdata) + +liste_matCorEtBlockSelect = matCorEtBlockSelect(res_block_splsda = mixomics_result, + cutoff_comp = args$cutoff_comp, + comp = 1:2) + +mat_cor_comp1 = liste_matCorEtBlockSelect$mat_cor_comp1 +mat_cor_comp2 = liste_matCorEtBlockSelect$mat_cor_comp2 +dataframe_cor_comp_var_global = liste_matCorEtBlockSelect$dataframe_cor_comp_var_global +liste_vec_indice_blockSelect = liste_matCorEtBlockSelect$liste_vec_indice_blockSelect +liste_vec_blocks = liste_matCorEtBlockSelect$liste_vec_blocks + +print("Mat cor comp1:") +print(mat_cor_comp1) +print("Mat cor comp2:") +print(mat_cor_comp2) +print("dataframe_cor_comp_var_global:") +print(dataframe_cor_comp_var_global) +print("liste_vec_indice_blockSelect:") +print(liste_vec_indice_blockSelect) +print("liste_vec_blocks:") +print(liste_vec_blocks) + + +lapply(liste_vec_blocks, write, file=args$output_blocks_comb, append=TRUE, ncolumns=100, sep=",") + + +print("Reading Mat Block Y") +mat_block_Y = read.table(args$mat_block_Y_file, header=TRUE, row.names=1) +print(mat_block_Y) + + +liste_dataframe_cor_comp_var_global = addVariablesReponses(res_block_splsda = mixomics_result, + dataframe_cor_comp_var_global = dataframe_cor_comp_var_global, + liste_vec_indice_blockSelect = liste_vec_indice_blockSelect, + mat_block_Y = mat_block_Y) + + +save(mixomics_result, + liste_matCorEtBlockSelect, + mat_cor_comp1, + mat_cor_comp2, + dataframe_cor_comp_var_global, + liste_vec_indice_blockSelect, + liste_vec_blocks, + liste_dataframe_cor_comp_var_global, + file = args$output_rdata)