# HG changeset patch
# User davidvanzessen
# Date 1463665373 14400
# Node ID 7696dd687f3982b016ee3c776b939663f4e7c855
# Parent  5eaead0a68c5151fafad7582c39cde0af2c53756
Uploaded

diff -r 5eaead0a68c5 -r 7696dd687f39 report_clonality/RScript.r
--- a/report_clonality/RScript.r	Tue May 17 03:22:16 2016 -0400
+++ b/report_clonality/RScript.r	Thu May 19 09:42:53 2016 -0400
@@ -579,11 +579,10 @@
 		clonalFreqSample = clonalFreq[clonalFreq$Sample == sample,]
 		if(max(clonalFreqSample$Type) > 1){
 			for(i in 2:max(clonalFreqSample$Type)){
-				clonalFreqSample = clonalFreqSample[clonalFreqSample$Type == i,]
-				print(clonalFreqSample[clonalFreqSample$Type == i,])
-				PRODF.sub = PRODF[PRODF$clonaltype %in% clonalFreqSample$clonaltype,]
-				PRODF.sub = PRODF.sub[order(PRODF.sub$clonaltype),]
-				write.table(PRODF.sub, file=paste("coincidences_", sample, "_", i, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
+				clonalFreqSampleType = clonalFreqSample[clonalFreqSample$Type == i,]
+				clonalityFrame.sub = clonalityFrame[clonalityFrame$clonaltype %in% clonalFreqSampleType$clonaltype,]
+				clonalityFrame.sub = clonalityFrame.sub[order(clonalityFrame.sub$clonaltype),]
+				write.table(clonalityFrame.sub, file=paste("coincidences_", sample, "_", i, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
 			}
 		}
 	}
@@ -644,6 +643,7 @@
     
     
     ClonalityOverviewPrint <- function(dat){
+	  dat = dat[order(dat[,2]),]
       write.table(dat[-1], paste("ClonalityOverView_", unique(dat[1])[1,1] , ".csv", sep=""), sep=",",quote=F,na="-",row.names=F,col.names=F)
     }