| Previous changeset 0:08aa67564858 (2014-01-28) Next changeset 2:f8f74848443e (2014-01-28) |
|
Commit message:
Uploaded |
|
modified:
RScript.r r_wrapper.sh |
| b |
| diff -r 08aa67564858 -r 81b9673b29be RScript.r --- a/RScript.r Tue Jan 28 03:44:44 2014 -0500 +++ b/RScript.r Tue Jan 28 06:57:38 2014 -0500 |
| [ |
| @@ -315,3 +315,32 @@ clonalityOverviewSplit = split(clonalityOverview, f=clonalityOverview$Sample) lapply(clonalityOverviewSplit, FUN=ClonalityOverviewPrint) } + +if("Functionality" %in% colnames(test)) +{ + newData = data.frame(data.table(PROD)[,list(unique=.N, + VH.DEL=mean(X3V.REGION.trimmed.nt.nb), + P1=mean(P3V.nt.nb), + N1=mean(N1.REGION.nt.nb), + P2=mean(P5D.nt.nb), + DEL.DH=mean(X5D.REGION.trimmed.nt.nb), + DH.DEL=mean(X3D.REGION.trimmed.nt.nb), + P3=mean(P3D.nt.nb), + N2=mean(N2.REGION.nt.nb), + P4=mean(P5J.nt.nb), + DEL.JH=mean(X5J.REGION.trimmed.nt.nb), + Total.Del=( mean(X3V.REGION.trimmed.nt.nb) + + mean(X5D.REGION.trimmed.nt.nb) + + mean(X3D.REGION.trimmed.nt.nb) + + mean(X5J.REGION.trimmed.nt.nb)), + + Total.N=( mean(N1.REGION.nt.nb) + + mean(N2.REGION.nt.nb)), + + Total.P=( mean(P3V.nt.nb) + + mean(P5D.nt.nb) + + mean(P3D.nt.nb) + + mean(P5J.nt.nb))), + by=c("Sample")]) + write.table(newData, "junctionAnalysis.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) +} \ No newline at end of file |
| b |
| diff -r 08aa67564858 -r 81b9673b29be r_wrapper.sh --- a/r_wrapper.sh Tue Jan 28 03:44:44 2014 -0500 +++ b/r_wrapper.sh Tue Jan 28 06:57:38 2014 -0500 |
| [ |
| @@ -15,10 +15,20 @@ echo "<img src='DPlot.png'/>" >> $2 echo "<img src='JPlot.png'/>" >> $2 +hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)" + +if [[ "$hasReplicateColumn" == "Yes" ]] ; then + echo "<table border='1'><th><td>Sample</td><td>unique</td><td>VH.DEL</td><td>P1</td><td>N1</td><td>P2</td><td>DEL.DH</td><td>DH.DEL</td><td>P3</td><td>N2</td><td>P4</td><td>DEL.JH</td><td>Total.Del</td><td>Total.N</td><td>Total.P</td></th>" >> $outputFile + while IFS=, Sample unique VH.DEL P1 N1 P2 DEL.DH DH.DEL P3 N2 P4 DEL.JH Total.Del Total.N Total.P + do + echo "<tr><td>$Sample</td><td>$unique</td><td>$VH.DEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DEL.DH</td><td>$DH.DEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DEL.JH</td><td>$Total.Del</td><td>$Total.N</td><td>$Total.P</td></tr>" >> $outputFile + done < $outputDir/junctionAnalysis.csv + echo "</table>" >> $outputFile +fi + samples=`cat $outputDir/samples.txt` count=1 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile -hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)" for sample in $samples; do clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)" echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile |