Mercurial > repos > ppericard > viscorvar

annotate viscorvar_matcoraddvar.R @ 2:c8533e9298e5 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
author ppericard
date Fri, 23 Oct 2020 10:15:56 +0000
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c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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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='Compute the matCorEtBlockSelect and addVariablesReponses functions')
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14 parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file")
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15 parser$add_argument('--cutoff_comp', dest='cutoff_comp', type='double', required=TRUE, help="")
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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('--block_Y_file', dest='block_Y_file', required=TRUE, help="Block Y filepath")
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18 parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file")
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19 parser$add_argument('--output_response_var', dest='output_response_var', required=TRUE, help="Output response variables file")
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20 parser$add_argument('--output_blocks_comb', dest='output_blocks_comb', required=TRUE, help="Output blocks combinations file")
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22 args <- parser$parse_args()
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24 ## Print parameters
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25 print("Input RData:")
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26 print(args$input_rdata)
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27 print("Cutoff comp:")
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28 print(args$cutoff_comp)
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29 print("Variables of interest:")
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30 print(args$interest_var_file)
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31 print("Block Y file:")
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32 print(args$block_Y_file)
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33 print("Output RData:")
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34 print(args$output_rdata)
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35 print("Output Response variables:")
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36 print(args$output_response_var)
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37 print("Output Blocks combinations:")
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38 print(args$output_blocks_comb)
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40 ## Loading libraries
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41 suppressPackageStartupMessages(require(visCorVar))
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43 # R script call
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44 source_local <- function(fname)
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45 {
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46 argv <- commandArgs(trailingOnly = FALSE)
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47 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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48 source(paste(base_dir, fname, sep="/"))
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49 }
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51 # Loading input Rdata file
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52 load(args$input_rdata)
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54 ncomp = mixomics_result$ncomp
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56 # Reading Block Y matrix
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57 print("Reading Block Y")
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58 mat_block_Y = read.table(args$block_Y_file, header=TRUE, row.names=1)
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59 print(mat_block_Y)
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61 response_var = colnames(mat_block_Y)
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62
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63 print("response_var:")
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64 print(response_var)
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66 # Write response variables to output file
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67 invisible(lapply(response_var, write, file=args$output_response_var, append=TRUE, ncolumns=1))
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69 # Reading var of intereset file
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70 interest_var_vec = NULL
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71 if (args$interest_var_file != 'None') {
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72 interest_var_vec = as.character(read.table(args$interest_var_file, header=FALSE)[[1]])
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73 }
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74
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75 #
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76 comp = 1:2
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78 # Running main function
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79 res_matCorAddVar = matCorAddVar(res_block_splsda = mixomics_result,
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80 block_Y = mat_block_Y,
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81 cutoff_comp = args$cutoff_comp,
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82 var_interest = interest_var_vec,
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83 comp = comp)
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84
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85 #
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86 mat_cor_comp1 = res_matCorAddVar$mat_cor_comp1
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87 mat_cor_comp2 = res_matCorAddVar$mat_cor_comp2
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88 list_vec_index_block_select = res_matCorAddVar$list_vec_index_block_select
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89 list_vec_names_blocks = res_matCorAddVar$list_vec_names_blocks
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90 list_cor_comp_selected_var_resp_var = res_matCorAddVar$list_cor_comp_selected_var_resp_var
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91 res_compute_cor_var_interest = res_matCorAddVar$res_compute_cor_var_interest
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92
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93 #
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94 print("mat_cor_comp1:")
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95 print(mat_cor_comp1)
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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96 print("mat_cor_comp2:")
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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97 print(mat_cor_comp2)
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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98 print("list_vec_index_block_select:")
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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99 print(list_vec_index_block_select)
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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100 print("list_vec_names_blocks:")
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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101 print(list_vec_names_blocks)
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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102 print("list_cor_comp_selected_var_resp_var:")
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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103 print(list_cor_comp_selected_var_resp_var)
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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104 print("res_compute_cor_var_interest:")
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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105 print(res_compute_cor_var_interest)
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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106
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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107 # Write all possible blocks combinations to output file
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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108 invisible(lapply(list_vec_names_blocks, write, file=args$output_blocks_comb, append=TRUE, ncolumns=100, sep=","))
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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109
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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110 # Save all objects in Rdata output file
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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111 save(res_matCorAddVar,
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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112 file = args$output_rdata)