# HG changeset patch
# User davidvanzessen
# Date 1469087812 14400
# Node ID 69a6bba9ada9ccc8bf3a10ae3dcc154079408358
# Parent  7696dd687f3982b016ee3c776b939663f4e7c855
Uploaded

diff -r 7696dd687f39 -r 69a6bba9ada9 report_clonality/RScript.r
--- a/report_clonality/RScript.r	Thu May 19 09:42:53 2016 -0400
+++ b/report_clonality/RScript.r	Thu Jul 21 03:56:52 2016 -0400
@@ -19,12 +19,12 @@
 library(data.table)
 
 if (!("reshape2" %in% rownames(installed.packages()))) {
-  install.packages("reshape2", repos="http://cran.xl-mirror.nl/") 
+  install.packages("reshape2", repos="http://cran.xl-mirror.nl/")
 }
 library(reshape2)
 
 if (!("lymphclon" %in% rownames(installed.packages()))) {
-  install.packages("lymphclon", repos="http://cran.xl-mirror.nl/") 
+  install.packages("lymphclon", repos="http://cran.xl-mirror.nl/")
 }
 library(lymphclon)
 
@@ -182,6 +182,16 @@
 
 write.table(x=count, file="productive_counting.txt", sep=",",quote=F,row.names=F,col.names=F)
 
+# ---------------------- V+J+CDR3 sequence count ----------------------
+
+VJCDR3.count = data.frame(table(clonalityFrame$Top.V.Gene, clonalityFrame$Top.J.Gene, clonalityFrame$CDR3.Seq.DNA))
+names(VJCDR3.count) = c("Top.V.Gene", "Top.J.Gene", "CDR3.Seq.DNA", "Count")
+
+VJCDR3.count = VJCDR3.count[VJCDR3.count$Count > 0,]
+VJCDR3.count = VJCDR3.count[order(-VJCDR3.count$Count),]
+
+write.table(x=VJCDR3.count, file="VJCDR3_count.txt", sep="\t",quote=F,row.names=F,col.names=T)
+
 # ---------------------- Frequency calculation for V, D and J ----------------------
 
 print("Report Clonality - frequency calculation V, D and J")
diff -r 7696dd687f39 -r 69a6bba9ada9 report_clonality/circos/circos.tar.gz
Binary file report_clonality/circos/circos.tar.gz has changed
diff -r 7696dd687f39 -r 69a6bba9ada9 report_clonality/r_wrapper.sh
--- a/report_clonality/r_wrapper.sh	Thu May 19 09:42:53 2016 -0400
+++ b/report_clonality/r_wrapper.sh	Thu Jul 21 03:56:52 2016 -0400
@@ -278,5 +278,7 @@
 	fi
 done
 
+echo "<tr><td>A frequency count of V Gene + J Gene + CDR3</td><td><a href='VJCDR3_count.txt'>Download</a></td></tr>" >> $outputFile
+
 echo "</table>" >> $outputFile
 echo "</div></html>" >> $outputFile