Mercurial > repos > sblanck > smagexp
annotate ImportDataFromMatrix.R @ 37:25b828010ca9 draft
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit bfd179bd7fb4796e21183e0e4de2fcf78ca35b7d
| author | sblanck |
|---|---|
| date | Mon, 25 Jun 2018 04:11:22 -0400 |
| parents | 7f74250a083d |
| children | c08b824e40cc |
| 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("--conditions",type="character",default=NULL,help="Text file summarizing conditions of the experiment (required)"), | |
| 14 make_option("--normalization",type="character",default=NULL,help="log2 transformation"), | |
| 15 make_option("--annotations",type="character",default="NULL",help="rdata object containing eset object"), | |
| 16 make_option("--rdataoutput",type="character",default="NULL",help="output rdata object containing eset object"), | |
| 17 make_option("--htmloutput",type="character",default=NULL,help="Output html report"), | |
| 18 make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"), | |
| 19 make_option("--htmltemplate",type="character",default="NULL",help="html template)") | |
| 20 | |
| 21 | |
| 22 ); | |
| 23 | |
| 24 | |
| 25 opt_parser = OptionParser(option_list=option_list); | |
| 26 opt = parse_args(opt_parser); | |
| 2 | 27 |
| 8 | 28 if(is.null(opt$input)){ |
| 29 print_help(opt_parser) | |
| 30 stop("input required.", call.=FALSE) | |
| 31 } | |
| 32 | |
| 33 if(is.null(opt$conditions)){ | |
| 34 print_help(opt_parser) | |
| 35 stop("conditions input required.", call.=FALSE) | |
| 36 } | |
| 37 | |
| 38 | |
| 39 #loading libraries | |
| 40 suppressPackageStartupMessages(require(GEOquery)) | |
| 2 | 41 |
| 8 | 42 suppressPackageStartupMessages(require(Biobase)) |
| 43 suppressPackageStartupMessages(require(GEOquery)) | |
| 44 suppressPackageStartupMessages(require(GEOmetadb)) | |
| 45 suppressPackageStartupMessages(require(limma)) | |
| 46 suppressPackageStartupMessages(require(jsonlite)) | |
| 47 suppressPackageStartupMessages(require(affy)) | |
| 48 suppressPackageStartupMessages(require(dplyr)) | |
| 49 suppressPackageStartupMessages(require(affyPLM)) | |
| 50 | |
| 51 dataFile=opt$input | |
| 52 normalization=opt$normalization | |
| 53 conditionsFile=opt$conditions | |
| 54 annotation=opt$annotations | |
| 55 result_export_eset=opt$rdataoutput | |
| 56 result=opt$htmloutput | |
| 57 result.path=opt$htmloutputpath | |
| 58 result.template=opt$htmltemplate | |
| 2 | 59 |
| 60 dir.create(result.path, showWarnings = TRUE, recursive = FALSE) | |
| 61 | |
| 8 | 62 data=as.matrix(read.table(file = dataFile,row.names=1,header=TRUE)) |
| 2 | 63 conditions=read.table(file=conditionsFile,sep = "\t",row.names=1) |
| 64 htmlfile=readChar(result.template, file.info(result.template)$size) | |
| 65 | |
| 66 colnames(conditions)=c("source_name_ch1","description") | |
| 67 phenodata<-new("AnnotatedDataFrame",data=conditions) | |
| 68 | |
| 69 eset=ExpressionSet(assayData=data,phenoData=phenodata,annotation=annotation) | |
| 70 | |
| 71 if (normalization == "quantile") { | |
|
37
25b828010ca9
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit bfd179bd7fb4796e21183e0e4de2fcf78ca35b7d
sblanck
parents:
8
diff
changeset
|
72 eset <- normalize.ExpressionSet.quantiles(eset, transfn="log") |
| 2 | 73 } else if (normalization == "log2") { |
| 74 exprs(eset) = log2(exprs(eset)) | |
| 75 } | |
| 76 | |
| 77 boxplotnorm="boxplotnorm.png" | |
| 78 png(boxplotnorm,width=800,height = 400) | |
| 79 par(mar=c(7,5,1,1)) | |
| 80 boxplot(data.frame(exprs(eset)),las=2,outline=FALSE) | |
| 81 dev.off() | |
| 82 htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOTNORM###",replacement = boxplotnorm, fixed = TRUE) | |
| 83 file.copy(boxplotnorm,result.path) | |
| 84 | |
| 85 plotMAnorm="plotMAnorm.png" | |
| 86 nblines=length(colnames(data))%/%3 + as.numeric((length(colnames(data))%%3)!=0) | |
| 87 png(plotMAnorm,width=800,height =300*nblines ) | |
| 88 par(mfrow=c(nblines,3)) | |
| 8 | 89 ##for (i in 1:length(colnames(data))){ |
| 2 | 90 MAplot(eset) |
| 91 #} | |
| 92 | |
| 93 dev.off() | |
| 94 htmlfile=gsub(x=htmlfile,pattern = "###PLOTMANORM###",replacement = plotMAnorm, fixed = TRUE) | |
| 95 file.copy(plotMAnorm,result.path) | |
| 96 #write.table(tolower(c(condition1Name,condition2Name)),quote = FALSE,col.names = FALSE, row.names=FALSE,file=result_export_conditions) | |
| 97 #saveConditions=c(condition1Name,condition2Name) | |
| 98 save(eset,file=result_export_eset) | |
| 99 write(htmlfile,result) | |
| 100 | |
| 101 #l=list() | |
| 102 #for(i in 1:length(esets)) | |
| 103 #{ | |
| 104 # l[[paste("study",i,sep="")]]<-res[[i]] | |
| 105 #} | |
| 106 #l[["Meta"]]=res[[length(res)-1]] | |
| 107 #showVenn(res,file.path(temp.files.path,"venn.png")) | |
| 108 #writeLines(c("<h2>Venn diagram</h2>"),file.conn) | |
| 109 #writeLines(c("<img src='venn.png'><br/><br/>"),file.conn) | |
| 110 #writeLines(c("</body></html>"),file.conn) | |
| 111 #close(file.conn) |