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annotate heatmap_wrapper.R @ 0:ad06aeed02c9 draft

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planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
author ethevenot
date Tue, 02 Aug 2016 06:26:41 -0400
parents
children b1667c118127
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ad06aeed02c9 planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
ethevenot
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1 #!/usr/bin/env Rscript
ad06aeed02c9 planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
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2
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3 library(batch) ## parseCommandArgs
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5 source_local <- function(fname){
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6 argv <- commandArgs(trailingOnly = FALSE)
ad06aeed02c9 planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
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7 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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8 source(paste(base_dir, fname, sep="/"))
ad06aeed02c9 planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
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9 }
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ad06aeed02c9 planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
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11 source_local("heatmap_script.R")
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13 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
ad06aeed02c9 planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
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16 ##------------------------------
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17 ## Initializing
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18 ##------------------------------
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19
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20 ## options
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21 ##--------
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23 strAsFacL <- options()[["stringsAsFactors"]]
ad06aeed02c9 planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
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24 options(stringsAsFactors=FALSE)
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26 ## constants
ad06aeed02c9 planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
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27 ##----------
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29 modNamC <- "Heatmap" ## module name
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31 ## log file
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32 ##---------
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33
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34 sink(argVc["information"])
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35
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36 cat("\nStart of the '", modNamC, "' module: ",
ad06aeed02c9 planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
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37 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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39 ## loading
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40 ##--------
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41
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42 proMN <- t(as.matrix(read.table(argVc["dataMatrix_in"],
ad06aeed02c9 planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
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43 check.names = FALSE,
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44 header = TRUE,
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45 row.names = 1,
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46 sep = "\t")))
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48 obsDF <- read.table(argVc["sampleMetadata_in"],
ad06aeed02c9 planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
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49 check.names = FALSE,
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50 header = TRUE,
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51 row.names = 1,
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52 sep = "\t")
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53
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54 feaDF <- read.table(argVc["variableMetadata_in"],
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55 check.names = FALSE,
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56 header = TRUE,
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57 row.names = 1,
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58 sep = "\t")
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59
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60 ## adding default parameter values
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61 ##--------------------------------
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62
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63
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64 if(!("corMetC" %in% names(argVc)))
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65 argVc["corMetC"] <- "pearson"
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66 if(!("aggMetC" %in% names(argVc)))
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67 argVc["aggMetC"] <- "ward"
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68 if(!("colC" %in% names(argVc)))
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69 argVc["colC"] <- "blueOrangeRed"
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70 if(!("scaL" %in% names(argVc)))
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71 argVc["scaL"] <- "TRUE"
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72 if(!("cexN" %in% names(argVc)))
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73 argVc["cexN"] <- "0.8"
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74
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75 ## checking
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76 ##---------
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77
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78 if(as.numeric(argVc["cutSamN"]) > nrow(proMN))
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79 stop("Number of sample clusters must be inferior to the number of samples")
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80 if(as.numeric(argVc["cutVarN"]) > ncol(proMN))
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81 stop("Number of variable clusters must be inferior to the number of variables")
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82
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83 ## printing arguments
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84 ##-------------------
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85
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86 cat("\nArguments used:\n\n")
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87 argMC <- as.matrix(argVc)
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88 colnames(argMC) <- "value"
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89 argDatVl <- grepl("\\.dat$", argVc) ## discarding dataset file names
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90 if(sum(argDatVl))
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91 argMC <- argMC[!argDatVl, , drop = FALSE]
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92 print(argMC)
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93
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94
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95 ##------------------------------
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96 ## Computation
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97 ##------------------------------
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98
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99
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100 heaLs <- heatmapF(proMN = proMN,
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101 obsDF = obsDF,
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102 feaDF = feaDF,
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103 disC = argVc["disC"],
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104 cutSamN = as.numeric(argVc["cutSamN"]),
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105 cutVarN = as.numeric(argVc["cutVarN"]),
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106 fig.pdfC = argVc["figure"],
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107 corMetC = argVc["corMetC"],
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108 aggMetC = argVc["aggMetC"],
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109 colC = argVc["colC"],
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110 scaL = as.logical(argVc["scaL"]),
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111 cexN = as.numeric(argVc["cexN"]))
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112
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113
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114 ##------------------------------
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115 ## Ending
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116 ##------------------------------
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117
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118
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119 ## saving
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120 ##-------
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121
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122 proDF <- cbind.data.frame(dataMatrix = colnames(heaLs[["proMN"]]),
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123 as.data.frame(t(heaLs[["proMN"]])))
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124 write.table(proDF,
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125 file = argVc["dataMatrix_out"],
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126 quote = FALSE,
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127 row.names = FALSE,
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128 sep = "\t")
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129
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130 obsDF <- cbind.data.frame(sampleMetadata = rownames(heaLs[["obsDF"]]),
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131 heaLs[["obsDF"]])
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132 write.table(obsDF,
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133 file = argVc["sampleMetadata_out"],
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134 quote = FALSE,
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135 row.names = FALSE,
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136 sep = "\t")
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137
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138 feaDF <- cbind.data.frame(variableMetadata = rownames(heaLs[["feaDF"]]),
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139 heaLs[["feaDF"]])
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140 write.table(feaDF,
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141 file = argVc["variableMetadata_out"],
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142 quote = FALSE,
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143 row.names = FALSE,
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144 sep = "\t")
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145
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146 ## Ending
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147 ##-------
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148
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149 cat("\nEnd of the '", modNamC, "' Galaxy module call: ",
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150 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep = "")
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151
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152 sink()
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153
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154 options(stringsAsFactors = strAsFacL)
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155
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156 rm(list = ls())