annotate CEMiTool.R @ 0:3f9ff31c88bb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
author iuc
date Mon, 10 Oct 2022 16:55:19 +0000
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children 81bffdf16b71
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3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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1 # Load all required libraries
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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2 library(CEMiTool, quietly = TRUE, warn.conflicts = FALSE)
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3 library(ggplot2, quietly = TRUE, warn.conflicts = FALSE)
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4 library(getopt, quietly = TRUE, warn.conflicts = FALSE)
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5 # setup R error handling to go to stderr
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6 options(
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7 show.error.messages = FALSE,
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8 error = function() {
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9 cat(geterrmessage(), file = stderr())
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10 q("no", 1, FALSE)
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11 }
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12 )
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14 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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15 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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17 ################################################################################
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18 ### Input Processing
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19 ################################################################################
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21 # Collect arguments from command line
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22 args <- commandArgs(trailingOnly = TRUE)
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23
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24 # Get options, using the spec as defined by the enclosed list.
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25 # Read the options from the default: commandArgs(TRUE).
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26 spec <- matrix(c(
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27 "expressionMatrix", "M", 1, "character",
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28 "sampleAnnotation", "A", 2, "character",
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29 "pathwayList", "P", 2, "character",
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30 "interactions", "I", 2, "character",
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31 "filter", "f", 1, "logical",
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32 "filter_pval", "i", 1, "numeric",
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33 "apply_vst", "a", 1, "logical",
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34 "n_genes", "n", 1, "integer",
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35 "eps", "e", 1, "numeric",
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36 "cor_method", "c", 1, "character",
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37 "cor_function", "y", 1, "character",
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38 "network_type", "x", 1, "character",
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39 "tom_type", "t", 1, "character",
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40 "merge_similar", "m", 1, "logical",
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41 "rank_method", "r", 1, "character",
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42 "min_ngen", "g", 1, "integer",
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43 "diss_thresh", "d", 1, "numeric",
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44 "center_func", "h", 1, "character",
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45 "ora_pval", "o", 1, "numeric",
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46 "gsea_scale", "l", 1, "logical",
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47 "gsea_min_size", "w", 1, "integer",
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48 "gsea_max_size", "z", 1, "integer",
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49 "sample_column_name", "v", 1, "character"),
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50 byrow = TRUE, ncol = 4
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51 )
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52
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53 opt <- getopt(spec)
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54 counts <- read.table(
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55 opt$expressionMatrix,
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56 header = TRUE,
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57 sep = "\t",
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58 strip.white = TRUE,
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59 stringsAsFactors = FALSE,
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60 check.names = FALSE
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61 )
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62
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63
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64 # Run CEMiTool
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65
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66 if (is.null(opt$sampleAnnotation)) {
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67 cem <- cemitool(
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68 counts,
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69 filter = opt$filter,
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70 filter_pval = opt$filter_pval,
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71 apply_vst = opt$apply_vst,
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72 n_genes = opt$n_genes,
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73 eps = opt$eps,
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74 cor_method = opt$cor_method,
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75 cor_function = opt$cor_function,
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76 network_type = opt$network_type,
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77 tom_type = opt$tom_type,
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78 merge_similar = opt$merge_similar,
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79 min_ngen = opt$min_ngen,
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80 diss_thresh = opt$diss_thresh,
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81 center_func = opt$center_func,
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82 verbose = TRUE,
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83 ora_pval = opt$ora_pval
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84 )
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85 } else {
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86 annotation <- read.table(
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87 opt$sampleAnnotation,
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88 header = TRUE,
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89 sep = "\t",
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90 strip.white = TRUE,
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91 stringsAsFactors = FALSE,
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92 check.names = FALSE
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93 )
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94 cem <- cemitool(
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95 counts,
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96 annotation,
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97 filter = opt$filter,
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98 filter_pval = opt$filter_pval,
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99 apply_vst = opt$apply_vst,
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100 n_genes = opt$n_genes,
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101 eps = opt$eps,
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102 cor_method = opt$cor_method,
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103 cor_function = opt$cor_function,
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104 network_type = opt$network_type,
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105 tom_type = opt$tom_type,
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106 merge_similar = opt$merge_similar,
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107 min_ngen = opt$min_ngen,
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108 diss_thresh = opt$diss_thresh,
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109 center_func = opt$center_func,
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110 verbose = TRUE,
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111 ora_pval = opt$ora_pval,
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112 sample_name_column = opt$sample_column_name,
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113 class_column = "Class",
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114 order_by_class = TRUE
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115 )
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116 cem <- mod_gsea(
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117 cem,
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118 gsea_scale = opt$gsea_scale,
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119 gsea_min_size = opt$gsea_min_size,
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120 gsea_max_size = opt$gsea_max_size,
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121 rank_method = opt$rank_method
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122 )
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123 cem <- plot_gsea(cem)
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124 }
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125
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126 if (!is.null(opt$pathwayList)) {
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127 gmt_in <- read_gmt(opt$pathwayList)
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128 cem <- mod_ora(cem, gmt_in)
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129 cem <- plot_ora(cem)
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130 }
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131
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132 if (!is.null(opt$interactions)) {
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133 interactions <- read.table(
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134 opt$interactions,
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135 header = TRUE,
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136 sep = "\t",
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137 strip.white = TRUE,
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138 stringsAsFactors = FALSE,
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139 check.names = FALSE
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140 )
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141 interactions_data(cem) <- interactions # add interactions
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142 cem <- plot_interactions(cem)
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143 }
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144
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145 ## Write analysis results into files
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146 write_files(cem,
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147 directory = "./Tables",
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148 force = TRUE)
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149
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150 generate_report(cem)
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151
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152 save_plots(cem,
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153 value = "all",
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154 directory = "./Plots",
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155 force = TRUE)