Mercurial > repos > davidvanzessen > report_clonality_igg
changeset 8:e2972f0935e9 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 26 Mar 2014 11:55:07 -0400 |
| parents | 1d0ed31089c6 |
| children | 712f3e9924d5 |
| files | RScript.r |
| diffstat | 1 files changed, 23 insertions(+), 3 deletions(-) [+] |
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--- a/RScript.r Tue Mar 25 07:08:12 2014 -0400 +++ b/RScript.r Wed Mar 26 11:55:07 2014 -0400 @@ -134,7 +134,9 @@ VGenes = merge(VGenes, TotalPerSample, by="Sample") VGenes$Frequency = VGenes$Count * 100 / VGenes$total VPlot = ggplot(VGenes) -VPlot = VPlot + geom_bar(aes( x = Top.V.Gene, y = Frequency, fill = Sample), stat='identity', position='dodge' ) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) +VPlot = VPlot + geom_bar(aes( x = Top.V.Gene, y = Frequency, fill = Sample), stat='identity', position='dodge' ) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + + ggtitle("Distribution of V gene families") + + ylab("Percentage of sequences") png("VFPlot.png") VPlot dev.off(); @@ -147,7 +149,9 @@ DGenes = merge(DGenes, TotalPerSample, by="Sample") DGenes$Frequency = DGenes$Count * 100 / DGenes$total DPlot = ggplot(DGenes) -DPlot = DPlot + geom_bar(aes( x = Top.D.Gene, y = Frequency, fill = Sample), stat='identity', position='dodge' ) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) +DPlot = DPlot + geom_bar(aes( x = Top.D.Gene, y = Frequency, fill = Sample), stat='identity', position='dodge' ) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + + ggtitle("Distribution of D gene families") + + ylab("Percentage of sequences") png("DFPlot.png") DPlot dev.off(); @@ -160,12 +164,28 @@ JGenes = merge(JGenes, TotalPerSample, by="Sample") JGenes$Frequency = JGenes$Count * 100 / JGenes$total JPlot = ggplot(JGenes) -JPlot = JPlot + geom_bar(aes( x = Top.J.Gene, y = Frequency, fill = Sample), stat='identity', position='dodge' ) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) +JPlot = JPlot + geom_bar(aes( x = Top.J.Gene, y = Frequency, fill = Sample), stat='identity', position='dodge' ) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + + ggtitle("Distribution of J gene families") + + ylab("Percentage of sequences") png("JFPlot.png") JPlot dev.off(); write.table(x=JGenes, file="JFFrequency.csv", sep=",",quote=F,row.names=F,col.names=T) +CDR3Length = data.frame(data.table(PRODF)[, list(Count=.N), by=c("Sample", "CDR3.Length.DNA")]) +TotalPerSample = data.frame(data.table(CDR3Length)[, list(total=sum(.SD$Count)), by=Sample]) +CDR3Length = merge(CDR3Length, TotalPerSample, by="Sample") +CDR3Length$Frequency = CDR3Length$Count * 100 / CDR3Length$total +CDR3LengthPlot = ggplot(CDR3Length) +CDR3LengthPlot = CDR3LengthPlot + geom_bar(aes( x = CDR3.Length.DNA, y = Frequency, fill = Sample), stat='identity', position='dodge' ) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + + ggtitle("Length distribution of CDR3") + + xlab("CDR3 Length") + + ylab("Percentage of sequences") +png("CDR3LengthPlot.png",width = 1280, height = 720) +CDR3LengthPlot +dev.off() +write.table(x=CDR3Length, file="CDR3LengthPlot.csv", sep=",",quote=F,row.names=F,col.names=T) + revVchain = Vchain revDchain = Dchain revVchain$chr.orderV = rev(revVchain$chr.orderV)