Mercurial > repos > ppericard > viscorvar

comparison networkVar_wrapper.R @ 0:d0b77b926863 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
author ppericard
date Tue, 23 Jun 2020 19:57:35 -0400
parents
children e93350dc99f1
comparison
equal deleted inserted replaced
-1:000000000000 0:d0b77b926863
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")