Mercurial > repos > davidvanzessen > combined_immune_repertoire_pipeline
changeset 10:a5c224bb0be5 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 10 Dec 2013 07:22:56 -0500 |
| parents | 8d83319a0f3d |
| children | a15d060a6248 |
| files | RScript.r |
| diffstat | 1 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/RScript.r Tue Dec 10 05:53:08 2013 -0500 +++ b/RScript.r Tue Dec 10 07:22:56 2013 -0500 @@ -93,7 +93,7 @@ setwd(outDir) -write.table(PRODF, "allUnique.tsv", sep="\t",quote=F,row.names=T,col.names=T) +write.table(PRODF, "allUnique.tsv", sep="\t",quote=F,row.names=F,col.names=T) pV = ggplot(PRODFV) pV = pV + geom_bar( aes( x=factor(reorder(Top.V.Gene, chr.orderV)), y=relFreq, fill=Sample), stat='identity', position="dodge") + theme(axis.text.x = element_text(angle = 90, hjust = 1)) @@ -236,17 +236,17 @@ clonalityFrame = PROD clonalityFrame$ReplicateConcat = do.call(paste, c(clonalityFrame[c("VDJCDR3", "Sample", "Replicate")], sep = ":")) clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$ReplicateConcat), ] - write.table(clonalityFrame, "clonalityComplete.tsv", sep="\t",quote=F,row.names=T,col.names=T) + write.table(clonalityFrame, "clonalityComplete.tsv", sep="\t",quote=F,row.names=F,col.names=T) ClonalitySampleReplicatePrint <- function(dat){ - write.table(dat, paste("clonality_", unique(dat$Sample) , "_", unique(dat$Replicate), ".tsv", sep=""), sep="\t",quote=F,row.names=T,col.names=T) + write.table(dat, paste("clonality_", unique(dat$Sample) , "_", unique(dat$Replicate), ".tsv", sep=""), sep="\t",quote=F,row.names=F,col.names=T) } clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")]) lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint) ClonalitySamplePrint <- function(dat){ - write.table(dat, paste("clonality_", unique(dat$Sample) , ".tsv", sep=""), sep="\t",quote=F,row.names=T,col.names=T) + write.table(dat, paste("clonality_", unique(dat$Sample) , ".tsv", sep=""), sep="\t",quote=F,row.names=F,col.names=T) } clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"])