Mercurial > repos > ppericard > mixomics_blocksplsda
comparison networkVar_wrapper.R @ 3:0a3c83f2197a draft
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
author | ppericard |
---|---|
date | Fri, 25 Oct 2019 07:10:59 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
2:655d1fbcd3e6 | 3:0a3c83f2197a |
---|---|
1 #!/usr/bin/env Rscript | |
2 | |
3 # Setup R error handling to go to stderr | |
4 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | |
5 | |
6 # we need that to not crash galaxy with an UTF8 error on German LC settings. | |
7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | |
8 | |
9 ## Get parameters ## | |
10 suppressPackageStartupMessages(require(argparse)) | |
11 | |
12 parser <- ArgumentParser(description='Run the networkVar function') | |
13 | |
14 parser$add_argument('--mat_similarity_rdata', dest='mat_similarity_rdata', required=TRUE, help="matSimilarity RData file") | |
15 parser$add_argument('--block_splsda_rdata', dest='block_splsda_rdata', required=TRUE, help="block.splsda RData file") | |
16 parser$add_argument('--var_list_file', dest='var_list_file', required=TRUE, help="Variables list file") | |
17 parser$add_argument('--interest_var_file', dest='interest_var_file', required=FALSE, help="Variables of interest file") | |
18 parser$add_argument('--responses_var', dest='responses_var', required=TRUE, help="Responses variables") | |
19 parser$add_argument('--output_graph', dest='output_graph', required=TRUE, help="Output graphml") | |
20 | |
21 args <- parser$parse_args() | |
22 | |
23 ## Print parameters | |
24 print("matSimilarity RData file:") | |
25 print(args$mat_similarity_rdata) | |
26 print("block.splsda RData file:") | |
27 print(args$block_splsda_rdata) | |
28 print("Variables list file:") | |
29 print(args$var_list_file) | |
30 print("Variables of interest:") | |
31 print(args$interest_var_file) | |
32 print("Response variables:") | |
33 print(args$responses_var) | |
34 print("Output graphml:") | |
35 print(args$output_graph) | |
36 | |
37 ## Loading libraries | |
38 suppressPackageStartupMessages(require(mixOmics)) | |
39 suppressPackageStartupMessages(require(igraph)) | |
40 | |
41 # R script call | |
42 source_local <- function(fname) | |
43 { | |
44 argv <- commandArgs(trailingOnly = FALSE) | |
45 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | |
46 source(paste(base_dir, fname, sep="/")) | |
47 } | |
48 ## Loading local functions | |
49 source_local("Integration_block_splsda_fonc.R") | |
50 | |
51 load(args$mat_similarity_rdata) | |
52 load(args$block_splsda_rdata) | |
53 | |
54 variables_vector = as.character(read.table(args$var_list_file, header=FALSE)[[1]]) | |
55 interest_var_vec = NULL | |
56 | |
57 if (args$interest_var_file != 'None') { | |
58 interest_var_vec = as.character(read.table(args$interest_var_file, header=FALSE)[[1]]) | |
59 } | |
60 | |
61 response_variables = strsplit(args$responses_var, ",")[[1]] | |
62 | |
63 print("Variables vector:") | |
64 print(variables_vector) | |
65 print("interest_var_vec:") | |
66 print(interest_var_vec) | |
67 print("response_variables:") | |
68 print(response_variables) | |
69 | |
70 network = networkVar(liste_matSimilarity_group = liste_matSimilarity_group, | |
71 comp = comp, | |
72 res_block_splsda = mixomics_result, | |
73 cutoff_comp = 0.8, | |
74 vec_varBlock = variables_vector, | |
75 vec_varRep = response_variables, | |
76 vec_varBlockInteret = interest_var_vec, | |
77 cutoff = 0) | |
78 | |
79 write.graph(network$gR, file = args$output_graph, format = "graphml") |