Mercurial > repos > ppericard > mixomics_blocksplsda

annotate 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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1 #!/usr/bin/env Rscript
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3 # Setup R error handling to go to stderr
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4 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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6 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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9 ## Get parameters ##
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10 suppressPackageStartupMessages(require(argparse))
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12 parser <- ArgumentParser(description='Run the networkVar function')
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14 parser$add_argument('--mat_similarity_rdata', dest='mat_similarity_rdata', required=TRUE, help="matSimilarity RData file")
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15 parser$add_argument('--block_splsda_rdata', dest='block_splsda_rdata', required=TRUE, help="block.splsda RData file")
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16 parser$add_argument('--var_list_file', dest='var_list_file', required=TRUE, help="Variables list file")
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17 parser$add_argument('--interest_var_file', dest='interest_var_file', required=FALSE, help="Variables of interest file")
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18 parser$add_argument('--responses_var', dest='responses_var', required=TRUE, help="Responses variables")
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19 parser$add_argument('--output_graph', dest='output_graph', required=TRUE, help="Output graphml")
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21 args <- parser$parse_args()
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23 ## Print parameters
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24 print("matSimilarity RData file:")
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25 print(args$mat_similarity_rdata)
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26 print("block.splsda RData file:")
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27 print(args$block_splsda_rdata)
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28 print("Variables list file:")
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29 print(args$var_list_file)
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30 print("Variables of interest:")
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31 print(args$interest_var_file)
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32 print("Response variables:")
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33 print(args$responses_var)
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34 print("Output graphml:")
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35 print(args$output_graph)
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37 ## Loading libraries
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38 suppressPackageStartupMessages(require(mixOmics))
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39 suppressPackageStartupMessages(require(igraph))
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41 # R script call
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42 source_local <- function(fname)
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43 {
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44 argv <- commandArgs(trailingOnly = FALSE)
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45 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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46 source(paste(base_dir, fname, sep="/"))
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47 }
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48 ## Loading local functions
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49 source_local("Integration_block_splsda_fonc.R")
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51 load(args$mat_similarity_rdata)
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52 load(args$block_splsda_rdata)
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54 variables_vector = as.character(read.table(args$var_list_file, header=FALSE)[[1]])
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55 interest_var_vec = NULL
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57 if (args$interest_var_file != 'None') {
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58 interest_var_vec = as.character(read.table(args$interest_var_file, header=FALSE)[[1]])
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59 }
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61 response_variables = strsplit(args$responses_var, ",")[[1]]
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63 print("Variables vector:")
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64 print(variables_vector)
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65 print("interest_var_vec:")
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66 print(interest_var_vec)
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67 print("response_variables:")
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68 print(response_variables)
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70 network = networkVar(liste_matSimilarity_group = liste_matSimilarity_group,
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71 comp = comp,
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72 res_block_splsda = mixomics_result,
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73 cutoff_comp = 0.8,
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74 vec_varBlock = variables_vector,
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75 vec_varRep = response_variables,
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76 vec_varBlockInteret = interest_var_vec,
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77 cutoff = 0)
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78
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79 write.graph(network$gR, file = args$output_graph, format = "graphml")