Mercurial > repos > sblanck > smagexp
annotate AffyQCnormalization.R @ 18:3d867f8a07ef draft
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 840095a764f473452cdef12053ca9b255267237e-dirty
| author | sblanck |
|---|---|
| date | Sat, 16 Dec 2017 10:18:15 -0500 |
| parents | ef7d98f9eb51 |
| children |
| rev | line source |
|---|---|
| 8 | 1 #!/usr/bin/env Rscript |
| 2 # setup R error handling to go to stderr | |
| 3 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | |
| 4 | |
| 5 # we need that to not crash galaxy with an UTF8 error on German LC settings. | |
| 6 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | |
| 7 | |
| 8 library("optparse") | |
| 9 | |
| 10 ##### Read options | |
| 11 option_list=list( | |
| 12 make_option("--input",type="character",default="NULL",help="rdata object containing eset object"), | |
| 13 make_option("--normalization",type="character",default=NULL,help="normalization method"), | |
| 14 make_option("--nbresult",type="character",default=NULL,help="number of result displayed results"), | |
| 15 make_option("--rdataoutput",type="character",default="NULL",help="output rdata object containing eset object"), | |
| 16 make_option("--htmloutput",type="character",default=NULL,help="Output html report"), | |
| 17 make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"), | |
| 18 make_option("--htmltemplate",type="character",default=NULL,help="html template)") | |
| 19 ); | |
| 2 | 20 |
| 8 | 21 opt_parser = OptionParser(option_list=option_list); |
| 22 opt = parse_args(opt_parser); | |
| 23 | |
| 24 if(is.null(opt$input)){ | |
| 25 print_help(opt_parser) | |
| 26 stop("input required.", call.=FALSE) | |
| 27 } | |
| 28 | |
| 29 #loading libraries | |
| 30 | |
| 31 suppressPackageStartupMessages(require(Biobase)) | |
| 32 suppressPackageStartupMessages(require(GEOquery)) | |
| 33 suppressPackageStartupMessages(require(GEOmetadb)) | |
| 34 suppressPackageStartupMessages(require(limma)) | |
| 35 suppressPackageStartupMessages(require(jsonlite)) | |
| 36 suppressPackageStartupMessages(require(affy)) | |
|
17
ef7d98f9eb51
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6
sblanck
parents:
8
diff
changeset
|
37 suppressPackageStartupMessages(require(affyPLM)) |
| 8 | 38 suppressPackageStartupMessages(require(dplyr)) |
| 39 | |
| 40 listInput <- trimws( unlist( strsplit(trimws(opt$input), ",") ) ) | |
| 41 | |
| 2 | 42 celList=vector() |
| 43 celFileNameList=vector() | |
| 8 | 44 |
| 45 for (i in 1:length(listInput)) | |
| 2 | 46 { |
| 8 | 47 inputFileInfo <- unlist( strsplit( listInput[i], ';' ) ) |
| 48 celList=c(celList,inputFileInfo[1]) | |
| 49 celFileNameList=c(celFileNameList,inputFileInfo[2]) | |
| 2 | 50 } |
| 51 | |
| 52 | |
| 8 | 53 normalization=opt$normalization |
| 54 result_export_eset=opt$rdataoutput | |
| 55 result=opt$htmloutput | |
| 56 result.path=opt$htmloutputpath | |
| 57 result.template=opt$htmltemplate | |
| 2 | 58 |
| 59 dir.create(result.path, showWarnings = TRUE, recursive = TRUE) | |
| 60 for(i in 1:length(celList)) | |
| 61 { | |
| 62 file.copy(celList[i],paste0("./",celFileNameList[i])) | |
| 63 } | |
| 64 | |
| 65 data <- ReadAffy(filenames=celFileNameList, celfile.path=".") | |
| 66 htmlfile=readChar(result.template, file.info(result.template)$size) | |
| 67 | |
| 68 boxplot="boxplot.png" | |
| 69 png(boxplot,width=800,height = 400) | |
| 70 par(mar=c(7,5,1,1)) | |
| 71 boxplot(data,las=2,outline=FALSE) | |
| 72 dev.off() | |
| 73 htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOT###",replacement = boxplot, fixed = TRUE) | |
| 74 file.copy(boxplot,result.path) | |
| 75 | |
| 76 images="images.png" | |
| 77 nblines=length(celList)%/%4 + as.numeric((length(celList)%%4)!=0) | |
| 78 png(images,width=800,height = 200*nblines) | |
| 79 par(mfrow=c(nblines,4)) | |
| 80 image(data) | |
| 81 dev.off() | |
| 82 htmlfile=gsub(x=htmlfile,pattern = "###IMAGES###",replacement = images, fixed = TRUE) | |
| 83 file.copy(images,result.path) | |
| 84 | |
| 85 | |
| 86 plotMA="plotMA.png" | |
| 87 nblines=length(celList)%/%3 + as.numeric((length(celList)%%3)!=0) | |
| 88 png(plotMA,width=800,height =300*nblines ) | |
| 89 par(mfrow=c(nblines,3)) | |
| 90 MAplot(data) | |
| 91 dev.off() | |
| 92 htmlfile=gsub(x=htmlfile,pattern = "###PLOTMA###",replacement = plotMA, fixed = TRUE) | |
| 93 file.copy(plotMA,result.path) | |
| 94 | |
| 95 | |
| 96 if (normalization == "rma") { | |
| 97 eset <- rma(data) | |
| 98 } else if (normalization == "quantile") { | |
| 99 eset = rma(data,background = FALSE,normalize = TRUE) | |
| 100 } else if (normalization == "background"){ | |
| 101 eset = rma(data,background = TRUE ,normalize = FALSE) | |
| 102 } else if (normalization == "log2") { | |
| 103 eset = rma(data,background = FALSE ,normalize = FALSE) | |
| 104 } | |
| 105 | |
| 106 | |
| 107 boxplotnorm="boxplotnorm.png" | |
| 108 png(boxplotnorm,width=800,height = 400) | |
| 109 par(mar=c(7,5,1,1)) | |
| 110 boxplot(data.frame(exprs(eset)),las=2,outline=FALSE) | |
| 111 dev.off() | |
| 112 htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOTNORM###",replacement = boxplotnorm, fixed = TRUE) | |
| 113 file.copy(boxplotnorm,result.path) | |
| 114 | |
| 115 plotMAnorm="plotMAnorm.png" | |
| 116 nblines=length(celList)%/%3 + as.numeric((length(celList)%%3)!=0) | |
| 117 png(plotMAnorm,width=800,height =300*nblines ) | |
| 118 par(mfrow=c(nblines,3)) | |
| 119 #for (i in 1:length(celList)){ | |
| 120 MAplot(eset) | |
| 121 #} | |
| 122 | |
| 123 dev.off() | |
| 124 htmlfile=gsub(x=htmlfile,pattern = "###PLOTMANORM###",replacement = plotMAnorm, fixed = TRUE) | |
| 125 file.copy(plotMAnorm,result.path) | |
| 126 save(eset,file=result_export_eset) | |
| 127 write(htmlfile,result) | |
| 128 |