Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 69:a59de79f6c0f draft
Uploaded
author | davidvanzessen |
---|---|
date | Mon, 08 Aug 2016 08:53:33 -0400 |
parents | 85a1d832d197 |
children | 6fdafffd7f0f |
files | complete_immunerepertoire.xml report_clonality/RScript.r report_clonality/r_wrapper.sh |
diffstat | 3 files changed, 32 insertions(+), 8 deletions(-) [+] |
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--- a/complete_immunerepertoire.xml Tue Aug 02 09:05:44 2016 -0400 +++ b/complete_immunerepertoire.xml Mon Aug 08 08:53:33 2016 -0400 @@ -10,13 +10,13 @@ #end for " $out_file $out_file.files_path "$clonaltype" #if $gene_selection.source == "imgtdb" - "${gene_selection.species}" "${gene_selection.locus}" $filterproductive $clonality_method + "${gene_selection.species}" "${gene_selection.locus}" $filterproductive ${clonality_method} #else "custom" "${gene_selection.vgenes};${gene_selection.dgenes};${gene_selection.jgenes}" $filterproductive $clonality_method #end if </command> <inputs> - <repeat name="patients" title="Patients" min="1" default="1"> + <repeat name="patients" title="Donor" min="1" default="1"> <repeat name="samples" title="Sample" min="1" default="1"> <param name="sample" type="data" label="Sample to Process" /> </repeat> @@ -32,7 +32,7 @@ </param> <conditional name="gene_selection" > - <param name="source" type="select" label="Gene reference" help="" > + <param name="source" type="select" label="Order of V(D)J genes in graphs" help="" > <option value="imgtdb" selected="true">IMGT-DB</option> <option value="custom">User defined</option> </param> @@ -98,16 +98,15 @@ </when> </conditional> - <param name="filterproductive" type="select" label="Filter out the unproductive sequences"> + <param name="filterproductive" type="select" label="Remove the unproductive sequences from graphs "> <option value="yes">Yes</option> <option value="no">No</option> </param> - + <param name="clonality_method" type="select" label="Old clonality algorithm or the newer R package"> <option value="old">Old</option> - <option value="boyd">R Package</option> + <option value="boyd">R Package (needs 3 replicate minimum)</option> </param> - </inputs> <outputs> <data format="html" name="out_file" />
--- a/report_clonality/RScript.r Tue Aug 02 09:05:44 2016 -0400 +++ b/report_clonality/RScript.r Mon Aug 08 08:53:33 2016 -0400 @@ -572,6 +572,8 @@ res[is.na(res)] = 0 infer.result = infer.clonality(as.matrix(res[,2:ncol(res)])) + print(infer.result) + write.table(data.table(infer.result[[12]]), file=paste("lymphclon_clonality_", sample_id, ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=F) res$type = rowSums(res[,2:ncol(res)]) @@ -775,6 +777,27 @@ PRODF = bak + +# ---------------------- D reading frame ---------------------- + +D.REGION.reading.frame = PRODF$D.REGION.reading.frame + +D.REGION.reading.frame[is.na(D.REGION.reading.frame)] = "No D" + +D.REGION.reading.frame = data.frame(table(D.REGION.reading.frame)) + +write.table(D.REGION.reading.frame, "DReadingFrame.csv" , sep="\t",quote=F,row.names=F,col.names=T) + +D.REGION.reading.frame = ggplot(D.REGION.reading.frame) +D.REGION.reading.frame = D.REGION.reading.frame + geom_bar(aes( x = D.REGION.reading.frame, y = Freq), stat='identity', position='dodge' ) + ggtitle("D reading frame") + xlab("Frequency") + ylab("Frame") + +png("DReadingFrame.png") +D.REGION.reading.frame +dev.off() + + + + # ---------------------- AA composition in CDR3 ---------------------- AACDR3 = PRODF[,c("Sample", "CDR3.Seq")]
--- a/report_clonality/r_wrapper.sh Tue Aug 02 09:05:44 2016 -0400 +++ b/report_clonality/r_wrapper.sh Mon Aug 08 08:53:33 2016 -0400 @@ -105,7 +105,9 @@ echo "<img src='DPlot.png'/>" >> $outputFile fi echo "<img src='JPlot.png'/>" >> $outputFile -echo "<img src='AAComposition.png'/></div>" >> $outputFile +echo "<img src='AAComposition.png'/>" >> $outputFile +echo "<img src='DReadingFrame.png'/>" >> $outputFile +echo "</div>" >> $outputFile #Heatmaps