Mercurial > repos > ppericard > mixomics_blocksplsda

annotate circleCor_wrapper.R @ 4:b0ab97ffc2a1 draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
author ppericard
date Mon, 09 Mar 2020 11:53:32 -0400
parents 0a3c83f2197a
children
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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 circleCor function')
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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('--blocks_vec', dest='blocks_vec', required=TRUE, help="Blocks vector")
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16 parser$add_argument('--responses_var', dest='responses_var', required=TRUE, help="Responses variables")
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17 parser$add_argument('--x_min', dest='x_min', type='double', required=TRUE, help="X min")
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18 parser$add_argument('--x_max', dest='x_max', type='double', required=TRUE, help="X max")
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19 parser$add_argument('--y_min', dest='y_min', type='double', required=TRUE, help="Y min")
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20 parser$add_argument('--y_max', dest='y_max', type='double', required=TRUE, help="Y max")
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21 parser$add_argument('--output_var', dest='output_var', required=TRUE, help="Output variables file")
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22 parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file")
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24 args <- parser$parse_args()
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26 ## Print parameters
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27 print("Input RData:")
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28 print(args$input_rdata)
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29 print("Blocks vector:")
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30 print(args$blocks_vec)
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31 print("Response variables:")
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32 print(args$responses_var)
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33 print("X min:")
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34 print(args$x_min)
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35 print("X max:")
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36 print(args$x_max)
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37 print("Y min:")
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38 print(args$y_min)
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39 print("Y max:")
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40 print(args$y_max)
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41 print("Output variables file:")
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42 print(args$output_var)
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43 print("Output PDF file:")
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44 print(args$output_pdf)
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46 ## Loading libraries
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47 suppressPackageStartupMessages(require(ellipse))
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48 suppressPackageStartupMessages(require(grDevices))
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49 suppressPackageStartupMessages(require(RColorBrewer))
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50 # suppressPackageStartupMessages(require(mixOmics))
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53 # R script call
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54 source_local <- function(fname)
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55 {
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56 argv <- commandArgs(trailingOnly = FALSE)
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57 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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58 source(paste(base_dir, fname, sep="/"))
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59 }
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60 ## Loading local functions
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61 source_local("Integration_block_splsda_fonc.R")
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63 load(args$input_rdata)
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64
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65 blocks_vector = strsplit(args$blocks_vec, ",")[[1]]
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66 response_variables = strsplit(args$responses_var, ",")[[1]]
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69 print("liste_vec_indice_blockSelect:")
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70 print(liste_vec_indice_blockSelect)
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71 print("liste_vec_blocks:")
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72 print(liste_vec_blocks)
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73 print("Mat cor comp1:")
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74 print(mat_cor_comp1)
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75 print("blocks_vector:")
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76 print(blocks_vector)
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77
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78
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79 # pdf(args$output_pdf, width=12, height=9)
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80 pdf(args$output_pdf)
3
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81
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82 mar = c(5.1, 4.1, 4.1, 9.1)
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83 par(mar = mar)
3
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84
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85 varSelect = circleCor(liste_dataframe_cor_comp_var_global = liste_dataframe_cor_comp_var_global,
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86 liste_vec_indice_blockSelect = liste_vec_indice_blockSelect,
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87 mat_cor_comp1 = mat_cor_comp1,
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88 mat_cor_comp2 = mat_cor_comp2,
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89 vec_blocks = blocks_vector,
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90 nomsVarReponses = response_variables,
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91 min.X = args$x_min,
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92 max.X = args$x_max,
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93 min.Y = args$y_min,
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94 max.Y = args$y_max,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
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95 cutoff = 0.85,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
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96 rad.in = 0.5,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
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97 cex = 0.7,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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98 cex_legend = 0.8,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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99 pos = c(1.2, 0),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
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100 pch = 20,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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parents:
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101 inset = c(-0.25, 0))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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102
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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103 dev.off()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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104
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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105 write(varSelect, file=args$output_var, ncolumns=1)