--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/viscorvar_networkvar.R	Fri Oct 23 10:15:56 2020 +0000
@@ -0,0 +1,78 @@
+#!/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 networkVar function')
+
+parser$add_argument('--mat_similarity_rdata', dest='mat_similarity_rdata', required=TRUE, help="matSimilarity RData file")
+parser$add_argument('--var_list_file', dest='var_list_file', required=TRUE, help="Variables list file")
+# parser$add_argument('--interest_var_file', dest='interest_var_file', required=FALSE, help="Variables of interest file")
+parser$add_argument('--response_var', dest='response_var', required=TRUE, help="Response variables")
+parser$add_argument('--output_graph', dest='output_graph', required=TRUE, help="Output graphml")
+
+args <- parser$parse_args()
+
+## Print parameters
+print("matSimilarity RData file:")
+print(args$mat_similarity_rdata)
+print("Variables list file:")
+print(args$var_list_file)
+# print("Variables of interest:")
+# print(args$interest_var_file)
+print("Response variables:")
+print(args$response_var)
+print("Output graphml:")
+print(args$output_graph)
+
+## Loading libraries
+# suppressPackageStartupMessages(require(mixOmics))
+suppressPackageStartupMessages(require(igraph))
+
+# R script call
+source_local <- function(fname)
+{
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep="/"))
+}
+
+## Loading local functions
+suppressPackageStartupMessages(require(visCorVar))
+
+# Loading input Rdata file
+# loads res_compute_mat_similarity object
+load(args$mat_similarity_rdata)
+
+#
+names_block_variables = as.character(read.table(args$var_list_file, header=FALSE)[[1]])
+names_response_variables = strsplit(args$response_var, ",")[[1]]
+
+# interest_var_vec = NULL
+# if (args$interest_var_file != 'None') {
+#     interest_var_vec = as.character(read.table(args$interest_var_file, header=FALSE)[[1]])
+# }
+
+print("names_block_variables:")
+print(names_block_variables)
+# print("interest_var_vec:")
+# print(interest_var_vec)
+print("names_response_variables:")
+print(names_response_variables)
+
+res_networkVar = networkVar(res_compute_mat_similarity = res_compute_mat_similarity,
+                            names_block_variables = names_block_variables,
+                            names_response_variables = names_response_variables,
+                            cutoff = 0)
+
+print("networkVar() completed")
+print("res_networkVar:")
+print(res_networkVar)
+
+write.graph(res_networkVar$gR, file = args$output_graph, format = "graphml")
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