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8
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1 #!/usr/bin/env Rscript
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2 # setup R error handling to go to stderr
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3 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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4
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5 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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6 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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7
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8 library("optparse")
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9
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10 ##### Read options
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11 option_list=list(
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12 make_option("--input",type="character",default="NULL",help="rdata object containing eset object"),
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13 make_option("--normalization",type="character",default=NULL,help="normalization method"),
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14 make_option("--nbresult",type="character",default=NULL,help="number of result displayed results"),
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15 make_option("--rdataoutput",type="character",default="NULL",help="output rdata object containing eset object"),
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16 make_option("--htmloutput",type="character",default=NULL,help="Output html report"),
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17 make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"),
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18 make_option("--htmltemplate",type="character",default=NULL,help="html template)")
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19 );
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2
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20
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8
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21 opt_parser = OptionParser(option_list=option_list);
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22 opt = parse_args(opt_parser);
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23
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24 if(is.null(opt$input)){
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25 print_help(opt_parser)
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26 stop("input required.", call.=FALSE)
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27 }
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28
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29 #loading libraries
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30
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31 suppressPackageStartupMessages(require(Biobase))
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32 suppressPackageStartupMessages(require(GEOquery))
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33 suppressPackageStartupMessages(require(GEOmetadb))
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34 suppressPackageStartupMessages(require(limma))
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35 suppressPackageStartupMessages(require(jsonlite))
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36 suppressPackageStartupMessages(require(affy))
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37 suppressPackageStartupMessages(library(affyPLM))
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38 suppressPackageStartupMessages(require(dplyr))
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39
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40 listInput <- trimws( unlist( strsplit(trimws(opt$input), ",") ) )
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41
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2
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42 celList=vector()
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43 celFileNameList=vector()
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8
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44
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45 for (i in 1:length(listInput))
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2
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46 {
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8
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47 inputFileInfo <- unlist( strsplit( listInput[i], ';' ) )
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48 celList=c(celList,inputFileInfo[1])
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49 celFileNameList=c(celFileNameList,inputFileInfo[2])
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2
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50 }
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51
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52
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8
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53 normalization=opt$normalization
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54 result_export_eset=opt$rdataoutput
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55 result=opt$htmloutput
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56 result.path=opt$htmloutputpath
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57 result.template=opt$htmltemplate
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2
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58
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59 dir.create(result.path, showWarnings = TRUE, recursive = TRUE)
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60 for(i in 1:length(celList))
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61 {
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62 file.copy(celList[i],paste0("./",celFileNameList[i]))
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63 }
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64
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65 data <- ReadAffy(filenames=celFileNameList, celfile.path=".")
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66 htmlfile=readChar(result.template, file.info(result.template)$size)
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67
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68 boxplot="boxplot.png"
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69 png(boxplot,width=800,height = 400)
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70 par(mar=c(7,5,1,1))
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71 boxplot(data,las=2,outline=FALSE)
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72 dev.off()
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73 htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOT###",replacement = boxplot, fixed = TRUE)
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74 file.copy(boxplot,result.path)
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75
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76 images="images.png"
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77 nblines=length(celList)%/%4 + as.numeric((length(celList)%%4)!=0)
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78 png(images,width=800,height = 200*nblines)
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79 par(mfrow=c(nblines,4))
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80 image(data)
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81 dev.off()
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82 htmlfile=gsub(x=htmlfile,pattern = "###IMAGES###",replacement = images, fixed = TRUE)
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83 file.copy(images,result.path)
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84
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85
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86 plotMA="plotMA.png"
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87 nblines=length(celList)%/%3 + as.numeric((length(celList)%%3)!=0)
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88 png(plotMA,width=800,height =300*nblines )
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89 par(mfrow=c(nblines,3))
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90 MAplot(data)
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91 dev.off()
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92 htmlfile=gsub(x=htmlfile,pattern = "###PLOTMA###",replacement = plotMA, fixed = TRUE)
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93 file.copy(plotMA,result.path)
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94
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95
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96 if (normalization == "rma") {
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97 eset <- rma(data)
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98 } else if (normalization == "quantile") {
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99 eset = rma(data,background = FALSE,normalize = TRUE)
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100 } else if (normalization == "background"){
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101 eset = rma(data,background = TRUE ,normalize = FALSE)
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102 } else if (normalization == "log2") {
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103 eset = rma(data,background = FALSE ,normalize = FALSE)
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104 }
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105
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106
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107 boxplotnorm="boxplotnorm.png"
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108 png(boxplotnorm,width=800,height = 400)
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109 par(mar=c(7,5,1,1))
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110 boxplot(data.frame(exprs(eset)),las=2,outline=FALSE)
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111 dev.off()
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112 htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOTNORM###",replacement = boxplotnorm, fixed = TRUE)
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113 file.copy(boxplotnorm,result.path)
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114
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115 plotMAnorm="plotMAnorm.png"
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116 nblines=length(celList)%/%3 + as.numeric((length(celList)%%3)!=0)
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117 png(plotMAnorm,width=800,height =300*nblines )
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118 par(mfrow=c(nblines,3))
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119 #for (i in 1:length(celList)){
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120 MAplot(eset)
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121 #}
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122
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123 dev.off()
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124 htmlfile=gsub(x=htmlfile,pattern = "###PLOTMANORM###",replacement = plotMAnorm, fixed = TRUE)
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125 file.copy(plotMAnorm,result.path)
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126 save(eset,file=result_export_eset)
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127 write(htmlfile,result)
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128
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