Mercurial > repos > ppericard > mixomics_blocksplsda

comparison networkVar_wrapper.R @ 3:0a3c83f2197a draft

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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
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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")