--- a/RScript.r	Mon Dec 02 10:56:47 2013 -0500
+++ b/RScript.r	Mon Dec 09 05:42:56 2013 -0500
@@ -90,6 +90,8 @@
 
 setwd(outDir)
 
+write.table(PRODF, "allUnique.tsv", sep="\t",quote=F,row.names=T,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))
 pV = pV + xlab("Summary of V gene") + ylab("Frequency") + ggtitle("Relative frequency of V gene usage")
@@ -231,6 +233,22 @@
 	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)
+
+	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)
+	}
+
+    clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")])
+    lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint)
+
+    ClonalitySamplePrint <- function(dat){
+	    write.table(dat, paste("clonality_", unique(dat$Sample) , ".tsv", sep=""), sep="\t",quote=F,row.names=T,col.names=T)
+	}
+
+    clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"])
+    lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint)
+
 	clonalFreq = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "VDJCDR3")])
 	clonalFreqCount = data.frame(data.table(clonalFreq)[, list(Count=.N), by=c("Sample", "Type")])
 	clonalFreqCount$realCount = clonalFreqCount$Type * clonalFreqCount$Count