Resolves #21

zoom : twice the confidence interval instead of once
IARCbioinfo · Sep 22, 2015 · 059bf69 · 059bf69
1 parent da9a220
commit 059bf69
Showing 1 changed file with 2 additions and 2 deletions.
diff --git 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)