# HG changeset patch
# User davidvanzessen
# Date 1461935325 14400
# Node ID 55f18bf19d72d9739583c59706aa40890c2499a6
# Parent  bd6fb6c03948201a194ea80e529a85c7815fd162
Uploaded

diff -r bd6fb6c03948 -r 55f18bf19d72 report_clonality/RScript.r
--- a/report_clonality/RScript.r	Thu Apr 28 08:11:04 2016 -0400
+++ b/report_clonality/RScript.r	Fri Apr 29 09:08:45 2016 -0400
@@ -158,13 +158,10 @@
 sample.count$perc_prod_un = round(sample.count$Productive_unique / sample.count$All * 100)
 
 sample.count = merge(sample.count , unprod.sample.count, by="Sample", all.x=T)
-print(sample.count)
 sample.count$perc_unprod = round(sample.count$Unproductive / sample.count$All * 100)
 sample.count = merge(sample.count, unprod.unique.sample.count, by="Sample", all.x=T)
 sample.count$perc_unprod_un = round(sample.count$Unproductive_unique / sample.count$All * 100)
 
-print(sample.count)
-
 #then sample/replicate
 rep.count = merge(input.rep.count, prod.rep.count, by=c("Sample", "Replicate"), all.x=T)
 rep.count$perc_prod = round(rep.count$Productive / rep.count$All * 100)
@@ -547,6 +544,7 @@
 if("Replicate" %in% colnames(inputdata)) #can only calculate clonality score when replicate information is available
 {
   print("Report Clonality - Clonality")
+  write.table(clonalityFrame, "clonalityComplete.csv", sep=",",quote=F,row.names=F,col.names=T)
   if(clonality_method == "boyd"){
     samples = split(clonalityFrame, clonalityFrame$Sample, drop=T)
    
@@ -573,9 +571,23 @@
       write.table(coincidence.table, file=paste("lymphclon_coincidences_", sample_id, ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=T)
     }
   } else {
-    write.table(clonalityFrame, "clonalityComplete.csv", sep=",",quote=F,row.names=F,col.names=T)
-      
     clonalFreq = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "clonaltype")])
+    
+    #write files for every coincidence group of >1
+    samples = unique(clonalFreq$Sample)
+    for(sample in samples){
+		clonalFreqSample = clonalFreq[clonalFreq$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$clonaltype),]
+				write.table(PRODF.sub, file=paste("coincidences_", sample, "_", i, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
+			}
+		}
+	}
+	
     clonalFreqCount = data.frame(data.table(clonalFreq)[, list(Count=.N), by=c("Sample", "Type")])
     clonalFreqCount$realCount = clonalFreqCount$Type * clonalFreqCount$Count
     clonalSum = data.frame(data.table(clonalFreqCount)[, list(Reads=sum(realCount)), by=c("Sample")])
@@ -657,9 +669,8 @@
   }
   
   
-  print(names(PRODF))
   #ensure certain columns are in the data (files generated with older versions of IMGT Loader)
-  col.checks = c("N3.REGION.nt.nb", "N4.REGION.nt.nb")
+  col.checks = c("N.REGION.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "N3.REGION.nt.nb", "N4.REGION.nt.nb")
   for(col.check in col.checks){
 	  if(!(col.check %in% names(PRODF))){
 		  print(paste(col.check, "not found adding new column"))
@@ -676,8 +687,6 @@
 	  }
   }
   
-  print(names(PRODF))
-  
   num_median = function(x, na.rm=T) { as.numeric(median(x, na.rm=na.rm)) }
   
   newData = data.frame(data.table(PRODF)[,list(unique=.N, 
diff -r bd6fb6c03948 -r 55f18bf19d72 report_clonality/r_wrapper.sh
--- a/report_clonality/r_wrapper.sh	Thu Apr 28 08:11:04 2016 -0400
+++ b/report_clonality/r_wrapper.sh	Fri Apr 29 09:08:45 2016 -0400
@@ -164,7 +164,6 @@
 			echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
 			while IFS=, read replicate reads squared
 			do
-				
 				echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
 			done < $outputDir/ReplicateReads_$sample.csv
 			
@@ -178,7 +177,12 @@
 			echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile
 			while IFS=, read type count weight weightedCount
 			do
-				echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
+				if [[ "$type" -eq "1" ]]; then
+					echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
+				else
+					echo "<tr><td><a href='coincidences_${sample}_${type}.txt'>$type</a></td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
+				fi
+				
 			done < $outputDir/ClonalityOverView_$sample.csv
 			echo "</table></div>" >> $outputFile
 		else