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2
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1 library(Biobase)
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2 library(GEOquery)
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3 library(GEOmetadb)
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4 library(limma)
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5 library(jsonlite)
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6 library(affy)
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7 library(affyPLM)
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8 library(dplyr)
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9
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10 cargs<-commandArgs()
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11 cargs<-cargs[(which(cargs=="--args")+1):length(cargs)]
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12 nbargs=length(cargs)
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13 celList=vector()
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14 celFileNameList=vector()
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15 for (i in seq(1,nbargs-7,2))
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16 {
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17 celList=c(celList,cargs[[i]])
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18 celFileNameList=c(celFileNameList,cargs[[i+1]])
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19 }
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20
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21
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22 normalization=cargs[[nbargs-6]]
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23 result_export_eset=cargs[[nbargs-5]]
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24 result=cargs[[nbargs-4]]
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25 result.path=cargs[[nbargs-3]]
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26 result.template=cargs[[nbargs-2]]
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27
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28 dir.create(result.path, showWarnings = TRUE, recursive = TRUE)
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29 for(i in 1:length(celList))
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30 {
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31 file.copy(celList[i],paste0("./",celFileNameList[i]))
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32 }
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33
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34 data <- ReadAffy(filenames=celFileNameList, celfile.path=".")
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35 htmlfile=readChar(result.template, file.info(result.template)$size)
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36
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37 boxplot="boxplot.png"
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38 png(boxplot,width=800,height = 400)
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39 par(mar=c(7,5,1,1))
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40 boxplot(data,las=2,outline=FALSE)
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41 dev.off()
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42 htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOT###",replacement = boxplot, fixed = TRUE)
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43 file.copy(boxplot,result.path)
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44
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45 images="images.png"
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46 nblines=length(celList)%/%4 + as.numeric((length(celList)%%4)!=0)
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47 png(images,width=800,height = 200*nblines)
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48 par(mfrow=c(nblines,4))
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49 image(data)
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50 dev.off()
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51 htmlfile=gsub(x=htmlfile,pattern = "###IMAGES###",replacement = images, fixed = TRUE)
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52 file.copy(images,result.path)
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53
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54
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55 plotMA="plotMA.png"
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56 nblines=length(celList)%/%3 + as.numeric((length(celList)%%3)!=0)
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57 png(plotMA,width=800,height =300*nblines )
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58 par(mfrow=c(nblines,3))
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59 MAplot(data)
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60 dev.off()
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61 htmlfile=gsub(x=htmlfile,pattern = "###PLOTMA###",replacement = plotMA, fixed = TRUE)
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62 file.copy(plotMA,result.path)
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63
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64
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65 if (normalization == "rma") {
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66 eset <- rma(data)
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67 } else if (normalization == "quantile") {
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68 eset = rma(data,background = FALSE,normalize = TRUE)
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69 } else if (normalization == "background"){
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70 eset = rma(data,background = TRUE ,normalize = FALSE)
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71 } else if (normalization == "log2") {
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72 eset = rma(data,background = FALSE ,normalize = FALSE)
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73 }
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74
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75
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76 boxplotnorm="boxplotnorm.png"
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77 png(boxplotnorm,width=800,height = 400)
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78 par(mar=c(7,5,1,1))
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79 boxplot(data.frame(exprs(eset)),las=2,outline=FALSE)
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80 dev.off()
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81 htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOTNORM###",replacement = boxplotnorm, fixed = TRUE)
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82 file.copy(boxplotnorm,result.path)
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83
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84 plotMAnorm="plotMAnorm.png"
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85 nblines=length(celList)%/%3 + as.numeric((length(celList)%%3)!=0)
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86 png(plotMAnorm,width=800,height =300*nblines )
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87 par(mfrow=c(nblines,3))
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88 #for (i in 1:length(celList)){
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89 MAplot(eset)
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90 #}
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91
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92 dev.off()
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93 htmlfile=gsub(x=htmlfile,pattern = "###PLOTMANORM###",replacement = plotMAnorm, fixed = TRUE)
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94 file.copy(plotMAnorm,result.path)
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95 #write.table(tolower(c(condition1Name,condition2Name)),quote = FALSE,col.names = FALSE, row.names=FALSE,file=result_export_conditions)
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96 #saveConditions=c(condition1Name,condition2Name)
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97 save(eset,file=result_export_eset)
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98 write(htmlfile,result)
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99
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100 #l=list()
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101 #for(i in 1:length(esets))
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102 #{
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103 # l[[paste("study",i,sep="")]]<-res[[i]]
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104 #}
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105 #l[["Meta"]]=res[[length(res)-1]]
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106 #showVenn(res,file.path(temp.files.path,"venn.png"))
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107 #writeLines(c("<h2>Venn diagram</h2>"),file.conn)
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108 #writeLines(c("<img src='venn.png'><br/><br/>"),file.conn)
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109 #writeLines(c("</body></html>"),file.conn)
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110 #close(file.conn) |
