# HG changeset patch
# User davidvanzessen
# Date 1454063392 18000
# Node ID 371c568408e9410afe87c92714ea5a98253dc569
# Parent  d3d4823c101a8706acec21d6f603f1a03312c7f0
Uploaded

diff -r d3d4823c101a -r 371c568408e9 complete.sh
diff -r d3d4823c101a -r 371c568408e9 report_clonality/RScript.r
--- a/report_clonality/RScript.r	Thu Jan 28 03:21:26 2016 -0500
+++ b/report_clonality/RScript.r	Fri Jan 29 05:29:52 2016 -0500
@@ -456,6 +456,11 @@
   completeVD = merge(VandDCount, cartegianProductVD, all.y=TRUE)
   completeVD = merge(completeVD, revVchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE)
   completeVD = merge(completeVD, Dchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE)
+  
+  if(any(fltr, na.rm=T)){
+    completeVD[fltr,"relLength"] = 1
+  } 
+  
   VDList = split(completeVD, f=completeVD[,"Sample"])
   lapply(VDList, FUN=plotVD)
 }
@@ -493,6 +498,12 @@
 completeVJ = merge(VandJCount, cartegianProductVJ, all.y=TRUE)
 completeVJ = merge(completeVJ, revVchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE)
 completeVJ = merge(completeVJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE)
+
+fltr = is.nan(completeVJ$relLength)
+if(any(fltr, na.rm=T)){
+  completeVJ[fltr,"relLength"] = 1
+}
+
 VJList = split(completeVJ, f=completeVJ[,"Sample"])
 lapply(VJList, FUN=plotVJ)
 
@@ -531,6 +542,12 @@
   completeDJ = merge(DandJCount, cartegianProductDJ, all.y=TRUE)
   completeDJ = merge(completeDJ, revDchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE)
   completeDJ = merge(completeDJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE)
+  
+  fltr = is.nan(completeDJ$relLength)
+  if(any(fltr, na.rm=T)){
+    completeDJ[fltr,"relLength"] = 1
+  }
+  
   DJList = split(completeDJ, f=completeDJ[,"Sample"])
   lapply(DJList, FUN=plotDJ)
 }