# HG changeset patch # User davidvanzessen # Date 1490694004 14400 # Node ID 7c33029fd63daf8e704a58aaaf4fa90a35a6a5e9 # Parent 3a76faa53c596c3ecd2b7843752776b0be9282ba Uploaded diff -r 3a76faa53c59 -r 7c33029fd63d report_clonality/RScript.r --- a/report_clonality/RScript.r Tue Mar 14 06:51:38 2017 -0400 +++ b/report_clonality/RScript.r Tue Mar 28 05:40:04 2017 -0400 @@ -302,7 +302,9 @@ png("VPlot.png",width = 1280, height = 720) pV -dev.off(); +dev.off() + +ggsave("VPlot.pdf", pV, width=13, height=7) if(useD){ pD = ggplot(PRODFD) @@ -313,7 +315,9 @@ png("DPlot.png",width = 800, height = 600) print(pD) - dev.off(); + dev.off() + + ggsave("DPlot.pdf", pD, width=10, height=7) } pJ = ggplot(PRODFJ) @@ -324,7 +328,9 @@ png("JPlot.png",width = 800, height = 600) pJ -dev.off(); +dev.off() + +ggsave("JPlot.pdf", pJ) # ---------------------- Now the frequency plots of the V, D and J families ---------------------- @@ -344,7 +350,9 @@ theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank()) png("VFPlot.png") VPlot -dev.off(); +dev.off() +ggsave("VFPlot.pdf", VPlot) + write.table(x=VGenes, file="VFFrequency.txt", sep="\t",quote=F,row.names=F,col.names=T) if(useD){ @@ -362,7 +370,9 @@ theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank()) png("DFPlot.png") print(DPlot) - dev.off(); + dev.off() + + ggsave("DFPlot.pdf", DPlot) write.table(x=DGenes, file="DFFrequency.txt", sep="\t",quote=F,row.names=F,col.names=T) } @@ -384,6 +394,9 @@ png("CDR3LengthPlot.png",width = 1280, height = 720) CDR3LengthPlot dev.off() + +ggsave("CDR3LengthPlot.pdf", CDR3LengthPlot, width=12, height=7) + write.table(x=CDR3Length, file="CDR3LengthPlot.txt", sep="\t",quote=F,row.names=F,col.names=T) # ---------------------- Plot the heatmaps ---------------------- @@ -413,6 +426,9 @@ png(paste("HeatmapVD_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Dchain$v.name)), height=100+(15*length(Vchain$v.name))) print(img) dev.off() + + ggsave(paste("HeatmapVD_", unique(dat[3])[1,1] , ".pdf", sep=""), img, height=13, width=8) + write.table(x=acast(dat, Top.V.Gene~Top.D.Gene, value.var="Length"), file=paste("HeatmapVD_", unique(dat[3])[1,1], ".txt", sep=""), sep="\t",quote=F,row.names=T,col.names=NA) } @@ -463,6 +479,9 @@ png(paste("HeatmapVJ_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Jchain$v.name)), height=100+(15*length(Vchain$v.name))) print(img) dev.off() + + ggsave(paste("HeatmapVJ_", unique(dat[3])[1,1] , ".pdf", sep=""), img, height=11, width=4) + 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) } @@ -512,6 +531,9 @@ png(paste("HeatmapDJ_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Jchain$v.name)), height=100+(15*length(Dchain$v.name))) print(img) dev.off() + + ggsave(paste("HeatmapDJ_", unique(dat[3])[1,1] , ".pdf", sep=""), img, width=4, height=7) + write.table(x=acast(dat, Top.D.Gene~Top.J.Gene, value.var="Length"), file=paste("HeatmapDJ_", unique(dat[3])[1,1], ".txt", sep=""), sep="\t",quote=F,row.names=T,col.names=NA) } @@ -903,7 +925,7 @@ D.REGION.reading.frame dev.off() - +ggsave("DReadingFrame.pdf", D.REGION.reading.frame) # ---------------------- AA composition in CDR3 ---------------------- @@ -937,11 +959,14 @@ AAfreqplot = AAfreqplot + annotate("rect", xmin = 5.5, xmax = 6.5, ymin = 0, ymax = Inf, fill = "blue", alpha = 0.2) AAfreqplot = AAfreqplot + annotate("rect", xmin = 6.5, xmax = 7.5, ymin = 0, ymax = Inf, fill = "red", alpha = 0.2) AAfreqplot = AAfreqplot + ggtitle("Amino Acid Composition in the CDR3") + xlab("Amino Acid, from Hydrophilic (left) to Hydrophobic (right)") + ylab("Percentage") + scale_fill_manual(values=sample.colors) -AAfreqplot = AAfreqplot + theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank()) +AAfreqplot = AAfreqplot + theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank()) png("AAComposition.png",width = 1280, height = 720) AAfreqplot dev.off() + +ggsave("AAComposition.pdf", AAfreqplot, width=12, height=7) + write.table(AAfreq, "AAComposition.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T) # ---------------------- AA median CDR3 length ---------------------- diff -r 3a76faa53c59 -r 7c33029fd63d report_clonality/circos/fonts.conf~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/report_clonality/circos/fonts.conf~ Tue Mar 28 05:40:04 2017 -0400 @@ -0,0 +1,8 @@ + +default = LTe50046.ttf +normal = LTe50046.ttf +bold = LTe50048.ttf +condensed = LTe50050.ttf +condensedbold = LTe50054.ttf +mono = pragmata.ttf +glyph = wingding.ttf diff -r 3a76faa53c59 -r 7c33029fd63d report_clonality/circos/housekeeping.conf~ diff -r 3a76faa53c59 -r 7c33029fd63d report_clonality/r_wrapper.sh --- a/report_clonality/r_wrapper.sh Tue Mar 14 06:51:38 2017 -0400 +++ b/report_clonality/r_wrapper.sh Tue Mar 28 05:40:04 2017 -0400 @@ -118,25 +118,25 @@ echo "
" >> $outputFile -echo "" >> $outputFile +echo "" >> $outputFile if [[ "$useD" == "true" ]] ; then - echo "" >> $outputFile + echo "" >> $outputFile fi -echo "" >> $outputFile +echo "" >> $outputFile if [[ "$useD" == "true" ]] ; then - echo "" >> $outputFile + echo "" >> $outputFile fi -echo "
" >> $outputFile +echo "
" >> $outputFile -echo "" >> $outputFile +echo "" >> $outputFile cat $dir/naive_gene_freq.htm >> $outputFile echo "
" >> $outputFile echo "
" >> $outputFile -echo "
" >> $outputFile -echo "" >> $outputFile +echo "
" >> $outputFile +echo "" >> $outputFile echo "" >> $outputFile @@ -158,11 +158,11 @@ for sample in $samples; do echo "
" >> $outputFile if [[ "$useD" == "true" ]] ; then - echo "" >> $outputFile + echo "" >> $outputFile fi - echo "" >> $outputFile + echo "" >> $outputFile if [[ "$useD" == "true" ]] ; then - echo "" >> $outputFile + echo "" >> $outputFile fi echo "
" >> $outputFile count=$((count+1)) @@ -194,11 +194,11 @@ for sample in $samples; do echo "
" >> $outputFile if [[ "$useD" == "true" ]] ; then - echo "
" >> $outputFile + echo "" >> $outputFile fi - echo "" >> $outputFile + echo "" >> $outputFile if [[ "$useD" == "true" ]] ; then - echo "" >> $outputFile + echo "" >> $outputFile fi echo "
V-D
V-D
V-J
V-J
D-J
D-J
" >> $outputFile count=$((count+1))