| Previous changeset 43:2325074a8461 (2017-10-26) Next changeset 45:942eea8359fe (2017-12-08) |
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Commit message:
Uploaded |
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modified:
report_clonality/RScript.r report_clonality/r_wrapper.sh |
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removed:
report_clonality/circos/circos.tar.gz |
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| diff -r 2325074a8461 -r 1d8728f3ff37 report_clonality/RScript.r --- a/report_clonality/RScript.r Thu Oct 26 09:58:05 2017 -0400 +++ b/report_clonality/RScript.r Fri Dec 08 05:47:33 2017 -0500 |
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| @@ -441,7 +441,7 @@ ylab("V Genes") + theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), panel.grid.major = element_line(colour = "gainsboro")) - png(paste("HeatmapVD_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Dchain$v.name)), height=100+(15*length(Vchain$v.name))) + png(paste("HeatmapVD_", unique(dat[3])[1,1] , ".png", sep=""), width=200+(15*length(Dchain$v.name)), height=100+(15*length(Vchain$v.name))) print(img) dev.off() @@ -458,16 +458,11 @@ VandDCount$relLength = VandDCount$l / VandDCount$max check = is.nan(VandDCount$relLength) if(any(check)){ - VandDCount[check,"relLength"] = 0 + VandDCount[check,"relLength"] = 0 } - - cartegianProductVD = expand.grid(Top.V.Gene = Vchain$v.name, Top.D.Gene = Dchain$v.name) - - completeVD = merge(VandDCount, cartegianProductVD, by.x=c("Top.V.Gene", "Top.D.Gene"), by.y=c("Top.V.Gene", "Top.D.Gene"), all=TRUE) - - completeVD = merge(completeVD, revVchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE) - - completeVD = merge(completeVD, Dchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE) + + completeVD = merge(VandDCount, revVchain, by.x="Top.V.Gene", by.y="v.name", all=TRUE) + completeVD = merge(completeVD, Dchain, by.x="Top.D.Gene", by.y="v.name", all=TRUE) fltr = is.nan(completeVD$relLength) if(all(fltr)){ @@ -494,7 +489,7 @@ ylab("V Genes") + theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), panel.grid.major = element_line(colour = "gainsboro")) - png(paste("HeatmapVJ_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Jchain$v.name)), height=100+(15*length(Vchain$v.name))) + png(paste("HeatmapVJ_", unique(dat[3])[1,1] , ".png", sep=""), width=200+(15*length(Jchain$v.name)), height=100+(15*length(Vchain$v.name))) print(img) dev.off() @@ -503,6 +498,8 @@ write.table(x=acast(dat, Top.V.Gene~Top.J.Gene, value.var="Length"), file=paste("HeatmapVJ_", unique(dat[3])[1,1], ".txt", sep=""), sep="\t",quote=F,row.names=T,col.names=NA) } + + VandJCount = data.frame(data.table(PRODF)[, list(Length=.N), by=c("Top.V.Gene", "Top.J.Gene", "Sample")]) VandJCount$l = log(VandJCount$Length) @@ -515,11 +512,8 @@ VandJCount[check,"relLength"] = 0 } -cartegianProductVJ = expand.grid(Top.V.Gene = Vchain$v.name, Top.J.Gene = Jchain$v.name) - -completeVJ = merge(VandJCount, cartegianProductVJ, all.y=TRUE) -completeVJ = merge(completeVJ, revVchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE) -completeVJ = merge(completeVJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE) +completeVJ = merge(VandJCount, revVchain, by.x="Top.V.Gene", by.y="v.name", all=TRUE) +completeVJ = merge(completeVJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all=TRUE) fltr = is.nan(completeVJ$relLength) if(any(fltr)){ @@ -546,7 +540,7 @@ ylab("D Genes") + theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), panel.grid.major = element_line(colour = "gainsboro")) - png(paste("HeatmapDJ_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Jchain$v.name)), height=100+(15*length(Dchain$v.name))) + png(paste("HeatmapDJ_", unique(dat[3])[1,1] , ".png", sep=""), width=200+(15*length(Jchain$v.name)), height=100+(15*length(Dchain$v.name))) print(img) dev.off() @@ -570,9 +564,8 @@ cartegianProductDJ = expand.grid(Top.D.Gene = Dchain$v.name, Top.J.Gene = Jchain$v.name) - completeDJ = merge(DandJCount, cartegianProductDJ, all.y=TRUE) - completeDJ = merge(completeDJ, revDchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE) - completeDJ = merge(completeDJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE) + completeDJ = merge(DandJCount, revDchain, by.x="Top.D.Gene", by.y="v.name", all=TRUE) + completeDJ = merge(completeDJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all=TRUE) fltr = is.nan(completeDJ$relLength) if(any(fltr)){ @@ -995,7 +988,7 @@ clonaltype.in.replicates = clonaltype.in.replicates[!(is.na(clonaltype.in.replicates$ID) | is.na(clonaltype.in.replicates$Top.V.Gene) | is.na(clonaltype.in.replicates$Top.J.Gene)),] clonaltype = unlist(strsplit(clonaltype, ",")) - clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[paste_columns], sep = ":")) + clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[clonaltype], sep = ":")) clonaltype.in.replicates = clonaltype.in.replicates[!duplicated(clonaltype.in.replicates$clonaltype),] |
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| diff -r 2325074a8461 -r 1d8728f3ff37 report_clonality/circos/circos.tar.gz |
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| Binary file report_clonality/circos/circos.tar.gz has changed |
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| diff -r 2325074a8461 -r 1d8728f3ff37 report_clonality/r_wrapper.sh --- a/report_clonality/r_wrapper.sh Thu Oct 26 09:58:05 2017 -0400 +++ b/report_clonality/r_wrapper.sh Fri Dec 08 05:47:33 2017 -0500 |
| [ |
| @@ -81,6 +81,12 @@ CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools" CIRCOSDIR="/home/galaxy/Anaconda3/bin" fi + + if [ -d "/media/galaxy/data/other_backup/circos/galaxian-circos//bin" ]; then #hopefully temporary fix #or not #really not + USECIRCOS="yes" + CIRCOSTOOLS="/media/galaxy/data/other_backup/circos/galaxian-circos/tools" + CIRCOSDIR="/media/galaxy/data/other_backup/circos/galaxian-circos/bin" + fi fi echo "Using Circos: $USECIRCOS" @@ -94,7 +100,12 @@ circos_file="$outputDir/${sample}_VJ_circos.txt" echo -e -n "labels$(cat ${circos_file})" > ${circos_file} + echo "Circos tools command:" + echo "cat \"${circos_file}\" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/" cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ + sed -i -- 's%/%:%g' $outputDir/circos/cells.txt + echo "Circos command:" + echo "$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1" $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png mv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg @@ -104,6 +115,7 @@ circos_file="$outputDir/${sample}_VD_circos.txt" echo -e -n "labels$(cat ${circos_file})" > ${circos_file} cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ + sed -i -- 's%/%:%g' $outputDir/circos/cells.txt $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg @@ -111,6 +123,7 @@ circos_file="$outputDir/${sample}_DJ_circos.txt" echo -e -n "labels$(cat ${circos_file})" > ${circos_file} cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ + sed -i -- 's%/%:%g' $outputDir/circos/cells.txt $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png mv $outputDir/circos/circos.svg $outputDir/circosDJ_${sample}.svg |