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Added entropy calculation to histogram of quality scores 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2316 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2009-12-10 21:57:35 +00:00
parent 2869270c11
commit 088363ce42
1 changed files with 4 additions and 2 deletions
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6
R/plot_residualError_QualityScoreCovariate.R
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@ -39,7 +39,9 @@ outfile = paste(input, ".quality_emp_hist.pdf", sep="")
pdf(outfile, height=7, width=7)
hst=subset(data.frame(e$Qempirical, e$nBases), e.nBases != 0)
hst2=subset(data.frame(f$Qempirical, f$nBases), f.nBases != 0)
plot(hst$e.Qempirical, hst$e.nBases, type="h", lwd=4, xlim=c(0,40), ylim=c(0,max(hst$e.nBases)), main="Empirical quality score histogram", xlab="Empirical quality score", ylab="Number of Bases",yaxt="n")
percentBases=hst$e.nBases / sum(as.numeric(hst$e.nBases))
entropy = -sum(log2(percentBases)*percentBases)
plot(hst$e.Qempirical, hst$e.nBases, type="h", lwd=4, xlim=c(0,40), ylim=c(0,max(hst$e.nBases)), main=paste("Empirical quality score histogram, entropy = ",round(entropy,digits=3)), xlab="Empirical quality score", ylab="Number of Bases",yaxt="n")
points(hst2$f.Qempirical, hst2$f.nBases, type="h", lwd=4, col="maroon1")
axis(2,axTicks(2), format(axTicks(2), scientific=F))
dev.off()
@ -52,7 +54,7 @@ outfile = paste(input, ".quality_rep_hist.pdf", sep="")
pdf(outfile, height=7, width=7)
hst=subset(data.frame(e$Qreported, e$nBases), e.nBases != 0)
hst2=subset(data.frame(f$Qreported, f$nBases), f.nBases != 0)
plot(hst$e.Qreported, hst$e.nBases, type="h", lwd=4, xlim=c(0,40), ylim=c(0,max(hst$e.nBases)), main="Reported quality score histogram", xlab="Reported quality score", ylab="Number of Bases",yaxt="n")
plot(hst$e.Qreported, hst$e.nBases, type="h", lwd=4, xlim=c(0,40), ylim=c(0,max(hst$e.nBases)), main=paste("Reported quality score histogram, entropy = ",round(entropy,digits=3)), xlab="Reported quality score", ylab="Number of Bases",yaxt="n")
points(hst2$f.Qreported, hst2$f.nBases, type="h", lwd=4, col="maroon1")
axis(2,axTicks(2), format(axTicks(2), scientific=F))
dev.off()