Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg
changeset 9:7dbc9ebcefce draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 12 Jan 2015 05:35:42 -0500 |
| parents | 043fd6613fd9 |
| children | b8db36cfe6ad |
| files | RScript.r r_wrapper.sh |
| diffstat | 2 files changed, 45 insertions(+), 4 deletions(-) [+] |
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--- a/RScript.r Mon Jan 12 04:32:40 2015 -0500 +++ b/RScript.r Mon Jan 12 05:35:42 2015 -0500 @@ -50,11 +50,14 @@ inputdata$Top.J.Gene = gsub("[*]([0-9]+)", "", inputdata$Top.J.Gene) inputdata$clonaltype = 1:nrow(inputdata) PRODF = inputdata +UNPROD = inputdata if(filterproductive){ if("Functionality" %in% colnames(inputdata)) { # "Functionality" is an IMGT column PRODF = inputdata[inputdata$Functionality == "productive" | inputdata$Functionality == "productive (see comment)", ] + UNPROD = inputdata[!(inputdata$Functionality == "productive" | inputdata$Functionality == "productive (see comment)"), ] } else { PRODF = inputdata[inputdata$VDJ.Frame != "In-frame with stop codon" & inputdata$VDJ.Frame != "Out-of-frame" & inputdata$CDR3.Found.How != "NOT_FOUND" , ] + UNPROD = inputdata[!(inputdata$VDJ.Frame != "In-frame with stop codon" & inputdata$VDJ.Frame != "Out-of-frame" & inputdata$CDR3.Found.How != "NOT_FOUND" ), ] } } @@ -62,6 +65,8 @@ if(clonaltype != "none"){ PRODF$clonaltype = do.call(paste, c(PRODF[unlist(strsplit(clonaltype, ","))], sep = ":")) PRODF = PRODF[!duplicated(PRODF$clonaltype), ] + UNPROD$clonaltype = do.call(paste, c(UNPROD[unlist(strsplit(clonaltype, ","))], sep = ":")) + UNPROD = UNPROD[!duplicated(UNPROD$clonaltype), ] } PRODF$freq = 1 @@ -576,5 +581,31 @@ mean(P3D.nt.nb, na.rm=T) + mean(P5J.nt.nb, na.rm=T))), by=c("Sample")]) - write.table(newData, "junctionAnalysis.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) + write.table(newData, "junctionAnalysisProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) + + newData = data.frame(data.table(UNPROD)[,list(unique=.N, + VH.DEL=mean(X3V.REGION.trimmed.nt.nb, na.rm=T), + P1=mean(P3V.nt.nb, na.rm=T), + N1=mean(N1.REGION.nt.nb, na.rm=T), + P2=mean(P5D.nt.nb, na.rm=T), + DEL.DH=mean(X5D.REGION.trimmed.nt.nb, na.rm=T), + DH.DEL=mean(X3D.REGION.trimmed.nt.nb, na.rm=T), + P3=mean(P3D.nt.nb, na.rm=T), + N2=mean(N2.REGION.nt.nb, na.rm=T), + P4=mean(P5J.nt.nb, na.rm=T), + DEL.JH=mean(X5J.REGION.trimmed.nt.nb, na.rm=T), + Total.Del=( mean(X3V.REGION.trimmed.nt.nb, na.rm=T) + + mean(X5D.REGION.trimmed.nt.nb, na.rm=T) + + mean(X3D.REGION.trimmed.nt.nb, na.rm=T) + + mean(X5J.REGION.trimmed.nt.nb, na.rm=T)), + + Total.N=( mean(N1.REGION.nt.nb, na.rm=T) + + mean(N2.REGION.nt.nb, na.rm=T)), + + Total.P=( mean(P3V.nt.nb, na.rm=T) + + mean(P5D.nt.nb, na.rm=T) + + mean(P3D.nt.nb, na.rm=T) + + mean(P5J.nt.nb, na.rm=T))), + by=c("Sample")]) + write.table(newData, "junctionAnalysisUnProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) }
--- a/r_wrapper.sh Mon Jan 12 04:32:40 2015 -0500 +++ b/r_wrapper.sh Mon Jan 12 05:35:42 2015 -0500 @@ -112,12 +112,22 @@ hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)" if [[ "$hasJunctionData" == "Yes" ]] ; then - echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table'><thead><tr><th>Sample</th><th>count</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile + echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile + echo "<table border='1' id='junction_table'> <caption>Productive</caption><thead><tr><th>Sample</th><th>count</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP do echo "<tr><td>$Sample</td><td>$unique</td><td>$VHDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELDH</td><td>$DHDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJH</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile - done < $outputDir/junctionAnalysis.csv - echo "</tbody></table></div>" >> $outputFile + done < $outputDir/junctionAnalysisProd.csv + echo "</tbody></table>" >> $outputFile + + echo "<table border='1' id='junction_table'> <caption>Unproductive</caption><thead><tr><th>Sample</th><th>count</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile + while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP + do + echo "<tr><td>$Sample</td><td>$unique</td><td>$VHDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELDH</td><td>$DHDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJH</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile + done < $outputDir/junctionAnalysisUnProd.csv + echo "</tbody></table>" >> $outputFile + + echo "</div>" >> $outputFile fi echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile