Mercurial > repos > sblanck > smagexp
annotate ImportDataFromMatrix.R @ 39:07ac07715f22 draft default tip
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 7026b0fbe3611962c37c7f9b5f001434f059e32c
| author | sblanck |
|---|---|
| date | Tue, 26 Jun 2018 04:14:25 -0400 |
| parents | c08b824e40cc |
| 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="log2 transformation"), | |
| 14 make_option("--annotations",type="character",default="NULL",help="rdata object containing eset object"), | |
| 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 | |
| 20 | |
| 21 ); | |
| 22 | |
| 23 | |
| 24 opt_parser = OptionParser(option_list=option_list); | |
| 25 opt = parse_args(opt_parser); | |
| 2 | 26 |
| 8 | 27 if(is.null(opt$input)){ |
| 28 print_help(opt_parser) | |
| 29 stop("input required.", call.=FALSE) | |
| 30 } | |
| 31 | |
| 32 | |
| 33 | |
| 34 #loading libraries | |
| 35 suppressPackageStartupMessages(require(Biobase)) | |
| 36 suppressPackageStartupMessages(require(limma)) | |
| 37 suppressPackageStartupMessages(require(jsonlite)) | |
| 38 suppressPackageStartupMessages(require(affy)) | |
| 39 suppressPackageStartupMessages(require(dplyr)) | |
| 40 suppressPackageStartupMessages(require(affyPLM)) | |
| 41 | |
| 42 dataFile=opt$input | |
| 43 normalization=opt$normalization | |
| 44 conditionsFile=opt$conditions | |
| 45 annotation=opt$annotations | |
| 46 result_export_eset=opt$rdataoutput | |
| 47 result=opt$htmloutput | |
| 48 result.path=opt$htmloutputpath | |
| 49 result.template=opt$htmltemplate | |
| 2 | 50 |
| 51 dir.create(result.path, showWarnings = TRUE, recursive = FALSE) | |
| 52 | |
| 8 | 53 data=as.matrix(read.table(file = dataFile,row.names=1,header=TRUE)) |
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c08b824e40cc
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 86c0c3bb957558f14e9400171640bf5a5c6605c9
sblanck
parents:
37
diff
changeset
|
54 #conditions=read.table(file=conditionsFile,sep = "\t",row.names=1) |
| 2 | 55 htmlfile=readChar(result.template, file.info(result.template)$size) |
| 56 | |
|
38
c08b824e40cc
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 86c0c3bb957558f14e9400171640bf5a5c6605c9
sblanck
parents:
37
diff
changeset
|
57 #colnames(conditions)=c("source_name_ch1","description") |
|
c08b824e40cc
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 86c0c3bb957558f14e9400171640bf5a5c6605c9
sblanck
parents:
37
diff
changeset
|
58 #phenodata<-new("AnnotatedDataFrame",data=conditions) |
| 2 | 59 |
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38
c08b824e40cc
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 86c0c3bb957558f14e9400171640bf5a5c6605c9
sblanck
parents:
37
diff
changeset
|
60 eset=ExpressionSet(assayData=data,annotation=annotation) |
| 2 | 61 |
| 62 if (normalization == "quantile") { | |
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25b828010ca9
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit bfd179bd7fb4796e21183e0e4de2fcf78ca35b7d
sblanck
parents:
8
diff
changeset
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63 eset <- normalize.ExpressionSet.quantiles(eset, transfn="log") |
| 2 | 64 } else if (normalization == "log2") { |
| 65 exprs(eset) = log2(exprs(eset)) | |
| 66 } | |
| 67 | |
| 68 boxplotnorm="boxplotnorm.png" | |
| 69 png(boxplotnorm,width=800,height = 400) | |
| 70 par(mar=c(7,5,1,1)) | |
| 71 boxplot(data.frame(exprs(eset)),las=2,outline=FALSE) | |
| 72 dev.off() | |
| 73 htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOTNORM###",replacement = boxplotnorm, fixed = TRUE) | |
| 74 file.copy(boxplotnorm,result.path) | |
| 75 | |
| 76 plotMAnorm="plotMAnorm.png" | |
| 77 nblines=length(colnames(data))%/%3 + as.numeric((length(colnames(data))%%3)!=0) | |
| 78 png(plotMAnorm,width=800,height =300*nblines ) | |
| 79 par(mfrow=c(nblines,3)) | |
| 8 | 80 ##for (i in 1:length(colnames(data))){ |
| 2 | 81 MAplot(eset) |
| 82 #} | |
| 83 | |
| 84 dev.off() | |
| 85 htmlfile=gsub(x=htmlfile,pattern = "###PLOTMANORM###",replacement = plotMAnorm, fixed = TRUE) | |
| 86 file.copy(plotMAnorm,result.path) | |
| 87 #write.table(tolower(c(condition1Name,condition2Name)),quote = FALSE,col.names = FALSE, row.names=FALSE,file=result_export_conditions) | |
| 88 #saveConditions=c(condition1Name,condition2Name) | |
| 89 save(eset,file=result_export_eset) | |
| 90 write(htmlfile,result) | |
| 91 | |
| 92 #l=list() | |
| 93 #for(i in 1:length(esets)) | |
| 94 #{ | |
| 95 # l[[paste("study",i,sep="")]]<-res[[i]] | |
| 96 #} | |
| 97 #l[["Meta"]]=res[[length(res)-1]] | |
| 98 #showVenn(res,file.path(temp.files.path,"venn.png")) | |
| 99 #writeLines(c("<h2>Venn diagram</h2>"),file.conn) | |
| 100 #writeLines(c("<img src='venn.png'><br/><br/>"),file.conn) | |
| 101 #writeLines(c("</body></html>"),file.conn) | |
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38
c08b824e40cc
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 86c0c3bb957558f14e9400171640bf5a5c6605c9
sblanck
parents:
37
diff
changeset
|
102 #close(file.conn) |