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Cmd line argument reference fix 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5761 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2011-05-04 20:00:14 +00:00
parent 5c6965575e
commit 1410327901
1 changed files with 6 additions and 6 deletions
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12
R/DataProcessingReport/Tearsheet.R
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@ -33,10 +33,10 @@ for(squid in squids){
samp<-rbind(samp, addsamps)
}
gsa.read.gatkreport(paste(evalroot, ".eval", sep=""))->FCeval
gsa.read.gatkreport(paste(evalroot, "extraFC.eval", sep=""))->FCeval
gsa.read.gatkreport(paste(evalroot, "extraFI.eval", sep=""))->FIeval
gsa.read.gatkreport(paste(evalroot, "extraSA.eval", sep=""))->SAeval
gsa.read.gatkreport(paste(cmdargs$evalroot, ".eval", sep=""))->FCeval
gsa.read.gatkreport(paste(cmdargs$evalroot, "extraFC.eval", sep=""))->FCeval
gsa.read.gatkreport(paste(cmdargs$evalroot, "extraFI.eval", sep=""))->FIeval
gsa.read.gatkreport(paste(cmdargs$evalroot, "extraSA.eval", sep=""))->SAeval
tearsheet<-function(){
@ -232,7 +232,7 @@ tearsheet<-function(){
par(mar=c(5, 5, 4, 2) + 0.1)
boxplot(eval.bysampleTITV.all$tiTvRatio, eval.bysampleTITV.known$tiTvRatio, eval.bysampleTITV.novel$tiTvRatio, main="Ti/Tv by Sample", col=c("dark gray", "blue", "red"), names=c("All", "Known", "Novel"), ylab="TI/TV per sample", main="",cex=1.3, cex.lab=1.3, cex.axis=1.3);
boxplot(eval.bysampleTITV.all$tiTvRatio, eval.bysampleTITV.known$tiTvRatio, eval.bysampleTITV.novel$tiTvRatio, main="Ti/Tv by Sample", col=c("dark gray", "blue", "red"), names=c("All", "Known", "Novel"), ylab="Ti/Tv per sample", main="",cex=1.3, cex.lab=1.3, cex.axis=1.3);
par(mar=c(7, 5, 4, 2) + 0.1)
ind = order(eval.bysample.all$nVariantLoci);
@ -251,7 +251,7 @@ tearsheet<-function(){
par(mar=c(5, 5, 4, 2) + 0.1)
barplot(eval.func$nVariantLoci[4:nrow(eval.func)], col=c("dark gray", "blue", "red"), space=c(.2,0,0), log="y", main="Variants by Functional Class", xlab="Functional Class", ylab="# Variants\n(axis in log space)")
barplot(eval.func$nVariantLoci[4:nrow(eval.func)], col=c("dark gray", "blue", "red"), space=c(.2,0,0), log="y", main="Variants by Functional Class", xlab="Functional Class", ylab="Number of variants\n(axis in log space)")
axis(1, at=c(1.5,5,8.5), lab=c("Missense", "Nonsense", "Silent"), cex=.5, tick=FALSE)
legend("top", c("All", "Known", "Novel"), fill=c("dark gray", "blue", "red"), cex=.7);