Mercurial > repos > ppericard > viscorvar

annotate networkVar_wrapper.R @ 0:d0b77b926863 draft

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