diff matCor_addVar_wrapper.R @ 3:0a3c83f2197a draft

planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty

--- /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)