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annotate NmrNormalization_wrapper.R @ 5:3d00a98974b7 draft

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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
author lecorguille
date Tue, 02 Oct 2018 12:14:47 -0400
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children 221cbd549c40
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3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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1 #!/usr/bin/env Rscript
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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3 ## 070115_NmrBucketing2galaxy_v1.R
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4 ## Marie Tremblay-Franco
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5 ## MetaboHUB: The French Infrastructure for Metabolomics and Fluxomics
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6 ## www.metabohub.fr/en
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7 ## marie.tremblay-franco@toulouse.inra.fr
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9 runExampleL <- FALSE
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12 ##------------------------------
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13 ## Options
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14 ##------------------------------
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15 strAsFacL <- options()$stringsAsFactors
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16 options(stringsAsFactors = FALSE)
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19 ##------------------------------
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20 ## Libraries laoding
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21 ##------------------------------
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22 # For parseCommandArgs function
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23 library(batch)
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25 # Constants
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26 argv <- commandArgs(trailingOnly = FALSE)
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27 script.path <- sub("--file=","",argv[grep("--file=",argv)])
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28 prog.name <- basename(script.path)
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29
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30 # Print help
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31 if (length(grep('-h', argv)) >0) {
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32 cat("Usage:", prog.name,
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33 "dataMatrix myDataMatrix.tsv",
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34 "scalingMethod PQN|QuantitativeVariable",
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35 "graphType None|Overlay|One_per_individual",
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36 "logOut myLog.txt",
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37 "dataMatrixOut myDataMatrixOutput.tsv",
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38 "graphOut myGraph.pdf",
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39 "\n")
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40 quit(status = 0)
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41 }
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42
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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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50 #Import the different functions
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51 source_local("NmrNormalization_script.R")
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52 source_local("DrawSpec.R")
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53
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55 ##------------------------------
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56 ## Errors ?????????????????????
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57 ##------------------------------
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58
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59
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60 ##------------------------------
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61 ## Constants
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62 ##------------------------------
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63 topEnvC <- environment()
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64 flagC <- "\n"
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65
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67 ##------------------------------
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68 ## Script
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69 ##------------------------------
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70 if(!runExampleL)
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71 argLs <- parseCommandArgs(evaluate=FALSE)
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72
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73
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74 ## Parameters Loading
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75 ##-------------------
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76 # Inputs
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77 data <- read.table(argLs[["dataMatrix"]], check.names=FALSE, header=TRUE, sep="\t", row.names=1)
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78 names <- rownames(data)
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79 ## Add a test to check if all values are numercical
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80 if (!all(vapply(data, is.numeric, FUN.VALUE = FALSE)))
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81 stop("Data are not numeric")
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82 ## Integer conversion to avoid stack overflow when computin the sum
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83 data <- as.data.frame(lapply(data, as.numeric))
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84 rownames(data) <- names
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85
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86 scaling <- argLs[["scalingMethod"]]
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87 graphique <- argLs[["graphType"]]
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88
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89 if (scaling=='PQN')
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90 {
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91 metadataSample <- read.table(argLs[["sampleMetadata"]],check.names=FALSE,header=TRUE,sep="\t")
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92 factor<- argLs[["factor"]]
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93 ControlGroup <- argLs[["controlGroup"]]
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94 }
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95 if (scaling=='QuantitativeVariable')
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96 {
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97 metadataSample <- read.table(argLs[["sampleMetadata"]],check.names=FALSE,header=TRUE,sep="\t")
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98 factor <- argLs[["factor"]]
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99 }
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100
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101 # Outputs
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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102 nomGraphe <- argLs[["graphOut"]]
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103 dataMatrixOut <- argLs[["dataMatrixOut"]]
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104 log <- argLs[["logOut"]]
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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105
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106
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107 ## Checking R packages
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108 ##--------------------
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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109 sink(log)
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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110 cat("\tPACKAGE INFO\n")
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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111 pkgs=c("batch")
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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112 for(pkg in pkgs) {
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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113 suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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114 cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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115 }
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116 cat("\n")
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117
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118
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119 ## Checking arguments
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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120 ##-------------------
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121 error.stock <- "\n"
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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122 if(length(error.stock) > 1)
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123 stop(error.stock)
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124
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125
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126 ## Computation
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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127 ##------------
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128 NormalizationResults <- NmrNormalization(dataMatrix=data,scalingMethod=scaling,sampleMetadata=metadataSample,
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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129 bioFactor=factor,ControlGroup=ControlGroup,
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130 graph=graphique,nomFichier=nomGraphe,savLog.txtC=log)
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131
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132 data_normalized <- NormalizationResults[[1]]
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133
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134
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135 ## Graphical outputs
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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136 ##------------------
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137 if (graphique != "None")
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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138 {
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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139 # Graphic Device opening
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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140 pdf(nomGraphe,onefile=TRUE)
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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141
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142 if (graphique == "Overlay")
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143 {
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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144 # Global spectral window
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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145 spectra <- data.frame(t(data_normalized))
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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146 drawSpec(spectra,xlab="", ylab="Intensity", main="")
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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147 }
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148 else
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149 {
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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150 for (i in 1:ncol(data_normalized))
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151 {
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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152 spectra <- t(data_normalized[,i])
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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153 drawSpec(spectra,xlab="", ylab="Intensity", main=colnames(data_normalized)[i])
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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154 }
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155 }
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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156 dev.off()
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157 }
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158
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159
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160 ## Saving
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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161 ##-------
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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162 # Data
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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163 data_normalized <- cbind(rownames(data_normalized),data_normalized)
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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164 colnames(data_normalized) <- c("Variable",colnames(data_normalized)[-1])
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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165 write.table(data_normalized,file=argLs$dataMatrixOut,quote=FALSE,row.names=FALSE,sep="\t")
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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166
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167
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168 ## Ending
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169 ##---------------------
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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170 cat("\nEnd of 'Normalization' Galaxy module call: ", as.character(Sys.time()), sep = "")
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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171 sink()
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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172 options(stringsAsFactors = strAsFacL)
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173 rm(list = ls())