Mercurial > repos > lecorguille > xcms_retcor
changeset 35:2b0a4c7a4a48 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
author | lecorguille |
---|---|
date | Thu, 05 Apr 2018 18:09:18 -0400 |
parents | 9714270678a7 |
children | e309e6af6744 |
files | lib.r xcms_retcor.r |
diffstat | 2 files changed, 23 insertions(+), 14 deletions(-) [+] |
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--- a/lib.r Tue Apr 03 11:39:48 2018 -0400 +++ b/lib.r Thu Apr 05 18:09:18 2018 -0400 @@ -28,8 +28,18 @@ } #@author G. Le Corguille +# This function merge several chromBPI or chromTIC into one. +mergeChrom <- function(chromTIC_merged, chromTIC, xdata_merged) { + if (is.null(chromTIC_merged)) return(NULL) + chromTIC_merged@.Data <- cbind(chromTIC_merged@.Data, chromTIC@.Data) + chromTIC_merged@phenoData <- xdata_merged@phenoData + return(chromTIC_merged) +} + +#@author G. Le Corguille # This function merge several xdata into one. mergeXData <- function(args) { + chromTIC <- NULL; chromBPI <- NULL for(image in args$images) { load(image) # Handle infiles @@ -47,6 +57,8 @@ singlefile_merged <- singlefile md5sumList_merged <- md5sumList sampleNamesList_merged <- sampleNamesList + chromTIC_merged <- chromTIC + chromBPI_merged <- chromBPI } else { if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata) else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata) @@ -55,6 +67,8 @@ md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin) sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin) sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames) + chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC, xdata_merged) + chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI, xdata_merged) } } rm(image) @@ -62,6 +76,8 @@ singlefile <- singlefile_merged; rm(singlefile_merged) md5sumList <- md5sumList_merged; rm(md5sumList_merged) sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged) + chromTIC <- chromTIC_merged; rm(chromTIC_merged) + chromBPI <- chromBPI_merged; rm(chromBPI_merged) if (!is.null(args$sampleMetadata)) { cat("\tXSET PHENODATA SETTING...\n") @@ -76,7 +92,7 @@ stop(error_message) } } - return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList)) + return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI)) } #@author G. Le Corguille @@ -176,9 +192,8 @@ return(myDataFrame) } -getPlotChromatogram <- function(xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") { +getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") { - chrom <- chromatogram(xdata, aggregationFun = aggregationFun) if (aggregationFun == "sum") type="Total Ion Chromatograms" else @@ -207,16 +222,6 @@ dev.off() } -#@author G. Le Corguille -getPlotTICs <- function(xdata, pdfname="TICs.pdf") { - getPlotChromatogram(xdata, pdfname, aggregationFun = "sum") -} - -#@author G. Le Corguille -getPlotBPIs <- function(xdata, pdfname="BPIs.pdf") { - getPlotChromatogram(xdata, pdfname, aggregationFun = "max") -} - # Get the polarities from all the samples of a condition #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
--- a/xcms_retcor.r Tue Apr 03 11:39:48 2018 -0400 +++ b/xcms_retcor.r Thu Apr 05 18:09:18 2018 -0400 @@ -49,6 +49,10 @@ singlefile <- rawFilePath$singlefile directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) +cat("\t\t\tCompute and Store TIC and BPI\n") +chromTIC_adjusted = chromatogram(xdata, aggregationFun = "sum") +chromBPI_adjusted = chromatogram(xdata, aggregationFun = "max") + cat("\n\n") @@ -89,7 +93,7 @@ cat("\n\n") #saving R data in .Rdata file to save the variables used in the present tool -objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList") +objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList", "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted") save(list=objects2save[objects2save %in% ls()], file="retcor.RData") cat("\n\n")