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annotate w4mcorcov_wrapper.R @ 14:90708fdbc22d draft default tip

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"planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
author eschen42
date Wed, 18 Nov 2020 18:53:37 +0000
parents 2ae2d26e3270
children
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1 #!/usr/bin/env Rscript
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3 # This script assumes that it is being executed in a current working directory containing the following files:
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4 # - w4mcorcov_lib.R
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5 # - w4mcorcov_input.R
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6 # - w4mcorcov_calc.R
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7 options(warn=1)
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8 ## constants
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9 ##----------
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11 modNamC <- "w4mcorcov" ## module name
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13 topEnvC <- environment()
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14 nl <- "\n"
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16 ## options
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17 ##--------
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19 strAsFacL <- options()$stringsAsFactors
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20 options(stringsAsFactors = FALSE)
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22 ## subroutines
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23 ##----------
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25 # from: https://github.com/molgenis/molgenis-pipelines/wiki/How-to-source-another_file.R-from-within-your-R-script
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26 LocationOfThisScript = function() # Function LocationOfThisScript returns the location of this .R script (may be needed to source other files in same dir)
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27 {
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28 this.file = NULL
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29 # This file may be 'sourced'
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30 for (i in -(1:sys.nframe())) {
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31 if (identical(sys.function(i), base::source)) this.file = (normalizePath(sys.frame(i)$ofile))
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32 }
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34 if (!is.null(this.file)) return(dirname(this.file))
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36 # But it may also be called from the command line
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37 cmd.args = commandArgs(trailingOnly = FALSE)
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38 cmd.args.trailing = commandArgs(trailingOnly = TRUE)
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39 cmd.args = cmd.args[seq.int(from=1, length.out=length(cmd.args) - length(cmd.args.trailing))]
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40 res = gsub("^(?:--file=(.*)|.*)$", "\\1", cmd.args)
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42 # If multiple --file arguments are given, R uses the last one
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43 res = tail(res[res != ""], 1)
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44 if (0 < length(res)) return(dirname(res))
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46 # Both are not the case. Maybe we are in an R GUI?
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47 return(NULL)
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48 }
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50 script.dir <- LocationOfThisScript()
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52 source(paste(script.dir, "w4mcorcov_lib.R", sep="/"))
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53 source(paste(script.dir, "w4mcorcov_util.R", sep="/"))
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54 source(paste(script.dir, "w4mcorcov_input.R", sep="/"))
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55 source(paste(script.dir, "w4mcorcov_salience.R", sep="/"))
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56 source(paste(script.dir, "w4mcorcov_calc.R", sep="/"))
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57 source(paste(script.dir, "w4mcorcov_output.R", sep="/"))
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59 ## log file
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60 ##---------
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62 my_log <- function(x, ...) { cat(paste(iso8601.znow(), " ", x, ..., nl, sep=""))}
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63 my_fatal <- function(x, ...) {
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64 my_log("ERROR: ", x, ...)
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65 quit(save = "no", status = 11, runLast = TRUE)
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66 }
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68 my_log("Start of the '", modNamC, "' Galaxy module call: ")
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71 ########
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72 # MAIN #
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73 ########
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74
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75 errorPrint(sessionInfo())
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76 errorCat("\nsearch path:")
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77 errorPrint(search())
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78 # errorCat("\nCurrently loaded namespaces:\n")
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79 # errorPrint(loadedNamespaces())
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80
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81 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
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82 errorCat("\n\n---\n\nArguments that were passed to R are as follows:\n")
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83 errorPrint(argVc)
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84
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85 my_env <- new.env()
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86
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87 ##------------------------------
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88 ## Initializing
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89 ##------------------------------
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90
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91 ## arguments
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92 ##----------
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93
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94 # files
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95
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96 my_env$dataMatrix_in <- as.character(argVc["dataMatrix_in"])
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97 my_env$sampleMetadata_in <- as.character(argVc["sampleMetadata_in"])
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98 my_env$variableMetadata_in <- as.character(argVc["variableMetadata_in"])
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99 my_env$contrast_detail <- as.character(argVc["contrast_detail"])
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100 my_env$contrast_corcov <- as.character(argVc["contrast_corcov"])
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101 my_env$contrast_salience <- as.character(argVc["contrast_salience"])
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102
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103 # other parameters
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104
2
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105 my_env$tesC <- as.character(argVc["tesC"])
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106 my_env$facC <- as.character(argVc["facC"])
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107 my_env$pairSigFeatOnly <- as.logical(argVc["pairSigFeatOnly"])
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108 my_env$levCSV <- as.character(argVc["levCSV"])
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109 my_env$matchingC <- as.character(argVc["matchingC"])
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110 my_env$labelFeatures <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL'
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111 my_env$min_crossval_i <- as.character(argVc["min_crossval_i"]) # Minumum number of samples for OPLS-DA cross-validation
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112 my_env$fdr_features <- as.character(argVc["fdr_features"]) # number of features to consider when adjusting p-value, or 'ALL'
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113 my_env$cplot_o <- as.logical(argVc["cplot_o"]) # TRUE if orthogonal C-plot is requested
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114 my_env$cplot_p <- as.logical(argVc["cplot_p"]) # TRUE if parallel C-plot is requested
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115 my_env$cplot_y <- as.character(argVc["cplot_y"]) # Choice of covariance/correlation for Y-axis on C-plot
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116
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117 label_features <- my_env$labelFeatures
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118 labelfeatures_check <- TRUE
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119 if ( is.na(label_features) ) {
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120 labelfeatures_check <- FALSE
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121 } else if ( is.null(label_features) ) {
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122 labelfeatures_check <- FALSE
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123 } else if (label_features != "ALL") {
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124 if ( is.na(as.numeric(label_features)) )
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125 labelfeatures_check <- FALSE
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126 else if ( as.numeric(label_features) < 0 )
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127 labelfeatures_check <- FALSE
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128 }
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129 if ( !labelfeatures_check ) {
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130 my_log("invalid argument: labelFeatures")
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131 print(label_features)
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132 quit(save = "no", status = 10, runLast = TRUE)
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133 }
0
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134
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135 min_crossval_i <- my_env$min_crossval_i
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136 crossval_check <- TRUE
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137 if ( is.na(min_crossval_i) ) {
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138 crossval_check <- FALSE
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139 } else if ( is.null(min_crossval_i) ) {
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140 crossval_check <- FALSE
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141 } else {
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142 if ( is.na(as.numeric(min_crossval_i)) )
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143 crossval_check <- FALSE
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144 else if ( as.numeric(min_crossval_i) < 0 )
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145 crossval_check <- FALSE
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146 }
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147 if ( !crossval_check ) {
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148 my_log("invalid argument: min_crossval_i")
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149 print(min_crossval_i)
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150 quit(save = "no", status = 10, runLast = TRUE)
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151 }
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152
0
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153 corcov_tsv_colnames <- TRUE
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154 corcov_tsv_append <- FALSE
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155 corcov_tsv_action <- function(tsv) {
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156 tsv_action_factory(
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157 file = my_env$contrast_corcov
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158 , colnames = corcov_tsv_colnames
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159 , append = corcov_tsv_append
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160 )(tsv)
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161 corcov_tsv_colnames <<- FALSE
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162 corcov_tsv_append <<- TRUE
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163 }
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164
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165 salience_tsv_colnames <- TRUE
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166 salience_tsv_append <- FALSE
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167 salience_tsv_action <- function(tsv) {
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168 tsv_action_factory(
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169 file = my_env$contrast_salience
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170 , colnames = salience_tsv_colnames
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171 , append = salience_tsv_append
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172 )(tsv)
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173 salience_tsv_colnames <<- FALSE
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174 salience_tsv_append <<- TRUE
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175 }
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176
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177 my_log( "-------------------------- Reading input data --------------------------")
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178
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179 # read_inputs is defined in w4mcorcov_input.R
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180 my_result <- read_inputs(input_env = my_env, failure_action = my_log)
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181
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182 if ( is.logical(my_result) && my_result) {
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183 my_log( "-------------------------- Beginning data processing --------------------------")
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184
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185 # receiver for result of the call to corcov_calc
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186 my_result <- NULL
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187
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188 # compute and plot the correlation_vs_covariance details plot
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189 # The parameter settings here are generally taken from bioconductor ropls::plot.opls source.
6
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190 if ( my_env$cplot_p || my_env$cplot_o ) {
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191 old_par <- par(
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192 font = 2 # bold font face
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193 , font.axis = 2 # bold font face for axis
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194 , font.lab = 2 # bold font face for x and y labels
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195 , lwd = 2 # line-width - interpretation is device spcific
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196 , pch = 18 # black diamond plot-character, see help for graphics::points
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197 , pty = "m" # do not force plots to be square
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198 , no.readonly = TRUE # only save writable parameters
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199 )
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200 pdf_height <- 12
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201 pdf_width <- 8
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202 my_layout <- function() {
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203 # lay out 2 columns by 3 rows with extra width at the margin of individual plots
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204 layout(
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205 matrix(
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206 # blank row plot 1 & 2 blank row plot 3 & 4 blank row plot 5 & 6 blank row
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207 c(0,0,0,0,0, 0,1,0,2,0, 0,0,0,0,0, 0,3,0,4,0, 0,0,0,0,0, 0,5,0,6,0, 0,0,0,0,0)
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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208 , nrow = 7
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209 , ncol = 5
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210 , byrow = TRUE
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211 )
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diff changeset
212 # slim columns 1, 3, and 5
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213 , widths = c(0.1, 0.9, 0.1, 0.9, 0.1)
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214 # slim rows 1, 3, 5, and 7
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215 , heights = c(0.1, 0.9, 0.1, 0.9, 0.1, 0.9, 0.1)
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216 )
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217 }
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218 } else {
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219 old_par <- par(
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220 font = 2 # bold font face
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221 , font.axis = 2 # bold font face for axis
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222 , font.lab = 2 # bold font face for x and y labels
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223 , lwd = 2 # line-width - interpretation is device spcific
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224 , pch = 18 # black diamond plot-character, see help for graphics::points
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225 , pty = "m" # do not force plots to be square
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226 , no.readonly = TRUE # only save writable parameters
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227 )
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228 pdf_height <- 8
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229 pdf_width <- 8
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230 my_layout <- function() {
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231 # lay out 2 columns by 2 rows with extra width at the margin of individual plots
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232 layout(
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233 matrix(
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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234 # blank row plot 1 & 2 blank row plot 3 & 4 blank row
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235 c(0,0,0,0,0, 0,1,0,2,0, 0,0,0,0,0, 0,3,0,4,0, 0,0,0,0,0)
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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236 , nrow = 5
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237 , ncol = 5
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238 , byrow = TRUE
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239 )
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
240 # slim columns 1, 3, and 5
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241 , widths = c(0.1, 0.9, 0.1, 0.9, 0.1)
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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242 # slim rows 1, 3, and 5
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243 , heights = c(0.1, 0.9, 0.1, 0.9, 0.1)
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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244 )
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245 }
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246 }
0
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247 plot2pdf(
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248 file.name = my_env$contrast_detail
6
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249 , width = pdf_width
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250 , height = pdf_height
0
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251 , plot.function = function() {
6
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252 # plot layout four or six plots per page
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253 my_layout()
0
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254 my_result <<- corcov_calc(
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255 calc_env = my_env
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256 , failure_action = my_fatal
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257 , progress_action = my_log
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258 , corcov_tsv_action = corcov_tsv_action
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259 , salience_tsv_action = salience_tsv_action
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260 )
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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261 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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262 )
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263 par(old_par)
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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264
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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265 my_log( "-------------------------- Finished data processing --------------------------")
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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266 }
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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267
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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268 my_log( "End of the '", modNamC, "' Galaxy module call")
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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269
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270 if (is.logical(my_result) && my_result) {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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271 quit(save = "no", status = 0, runLast = TRUE)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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272 } else {
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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273 my_log("failure :(")
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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274 quit(save = "no", status = 10, runLast = TRUE)
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275 }