Mercurial > repos > ppericard > viscorvar
comparison networkVar_wrapper.R @ 0:d0b77b926863 draft
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
author | ppericard |
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date | Tue, 23 Jun 2020 19:57:35 -0400 |
parents | |
children | e93350dc99f1 |
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-1:000000000000 | 0:d0b77b926863 |
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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('--var_list_file', dest='var_list_file', required=TRUE, help="Variables list file") | |
16 # parser$add_argument('--interest_var_file', dest='interest_var_file', required=FALSE, help="Variables of interest file") | |
17 parser$add_argument('--response_var', dest='response_var', required=TRUE, help="Response variables") | |
18 parser$add_argument('--output_graph', dest='output_graph', required=TRUE, help="Output graphml") | |
19 | |
20 args <- parser$parse_args() | |
21 | |
22 ## Print parameters | |
23 print("matSimilarity RData file:") | |
24 print(args$mat_similarity_rdata) | |
25 print("Variables list file:") | |
26 print(args$var_list_file) | |
27 # print("Variables of interest:") | |
28 # print(args$interest_var_file) | |
29 print("Response variables:") | |
30 print(args$response_var) | |
31 print("Output graphml:") | |
32 print(args$output_graph) | |
33 | |
34 ## Loading libraries | |
35 # suppressPackageStartupMessages(require(mixOmics)) | |
36 suppressPackageStartupMessages(require(igraph)) | |
37 | |
38 # R script call | |
39 source_local <- function(fname) | |
40 { | |
41 argv <- commandArgs(trailingOnly = FALSE) | |
42 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | |
43 source(paste(base_dir, fname, sep="/")) | |
44 } | |
45 | |
46 ## Loading local functions | |
47 # source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R") | |
48 install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.3.tar.gz", repos=NULL) | |
49 suppressPackageStartupMessages(require(visCorVar)) | |
50 print("visCorVar has been loaded") | |
51 | |
52 # Loading input Rdata file | |
53 # loads res_compute_mat_similarity object | |
54 load(args$mat_similarity_rdata) | |
55 | |
56 # | |
57 names_block_variables = as.character(read.table(args$var_list_file, header=FALSE)[[1]]) | |
58 names_response_variables = strsplit(args$response_var, ",")[[1]] | |
59 | |
60 # interest_var_vec = NULL | |
61 # if (args$interest_var_file != 'None') { | |
62 # interest_var_vec = as.character(read.table(args$interest_var_file, header=FALSE)[[1]]) | |
63 # } | |
64 | |
65 print("names_block_variables:") | |
66 print(names_block_variables) | |
67 # print("interest_var_vec:") | |
68 # print(interest_var_vec) | |
69 print("names_response_variables:") | |
70 print(names_response_variables) | |
71 | |
72 res_networkVar = networkVar(res_compute_mat_similarity = res_compute_mat_similarity, | |
73 names_block_variables = names_block_variables, | |
74 names_response_variables = names_response_variables, | |
75 cutoff = 0) | |
76 | |
77 print("networkVar() completed") | |
78 print("res_networkVar:") | |
79 print(res_networkVar) | |
80 | |
81 write.graph(res_networkVar$gR, file = args$output_graph, format = "graphml") |