From 059bf691ffbb692c45ff8462703b61a3771f3588 Mon Sep 17 00:00:00 2001 From: Tiffany Delhomme Date: Tue, 22 Sep 2015 17:00:38 +0200 Subject: [PATCH] Resolves #21 zoom : twice the confidence interval instead of once --- bin/pileup_nbrr_caller_vcf.r | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/pileup_nbrr_caller_vcf.r b/bin/pileup_nbrr_caller_vcf.r index 19b3417..fb5c076 100755 --- a/bin/pileup_nbrr_caller_vcf.r +++ b/bin/pileup_nbrr_caller_vcf.r @@ -214,7 +214,7 @@ plot_rob_nb <- function(rob_nb_res,qthreshold=0.01,plot_title=NULL,sbs,SB_thresh plot(rob_nb_res$coverage, rob_nb_res$ma_count, pch=21,bg=cols,col=outliers_color,xlab="Coverage (DP)",ylab="Number of ALT reads (AO)", - main=plot_title, ylim=c(0,yi1), xlim=c(0,xi)) + main=plot_title, ylim=c(0,2*yi1), xlim=c(0,xi)) mtext("zoom on 99% confidence interval") abline(a=0, b=yi1/xi, lwd=2, lty=3, col="blue") abline(a=0, b=yi2/xi, lwd=2, lty=3, col="blue") @@ -225,7 +225,7 @@ plot_rob_nb <- function(rob_nb_res,qthreshold=0.01,plot_title=NULL,sbs,SB_thresh plot(logqvals,rob_nb_res$ma_count/rob_nb_res$coverage,pch=21,bg=cols,col=outliers_color,ylab="Allelic fraction (AF)",xlab=bquote("log"[10] ~ "(q-value)"),main="Allelic fraction effect") abline(v=log10(qthreshold),col="red",lwd=2) - plot(logqvals,rob_nb_res$ma_count/rob_nb_res$coverage,pch=21,bg=cols,col=outliers_color,ylab="Allelic fraction (AF)",xlab=bquote("log"[10] ~ "(q-value)"),main="Allelic fraction effect", ylim=c(0,yi1/xi)) + plot(logqvals,rob_nb_res$ma_count/rob_nb_res$coverage,pch=21,bg=cols,col=outliers_color,ylab="Allelic fraction (AF)",xlab=bquote("log"[10] ~ "(q-value)"),main="Allelic fraction effect", ylim=c(0,(2*yi1)/xi)) mtext("zoom on 99% confidence interval") abline(v=log10(qthreshold),col="red",lwd=2)