Mercurial > repos > geert-vandeweyer > coverage_report

diff CoverageReport.pl @ 22:95062840f80f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Correction to png calls to use cairo instead of x11. thanks to Eric Enns for pointing this out.
author geert-vandeweyer
date Mon, 17 Nov 2014 07:10:11 -0500
parents 86df3f847a72
children fd788f9db899
line wrap: on
line diff
--- a/CoverageReport.pl	Thu Nov 06 04:28:02 2014 -0500
+++ b/CoverageReport.pl	Mon Nov 17 07:10:11 2014 -0500
@@ -208,7 +208,7 @@
 open OUT, ">$wd/Rout/boxplot.R";
 print OUT 'coverage <- read.table("../Targets.Global.Coverage",as.is=TRUE,sep="\t",header=FALSE)'."\n";
 print OUT 'coverage <- coverage[,'.$covcol.']'."\n";
-print OUT 'png(file="../Plots/CoverageBoxPlot.png", bg="white", width=240, height=480)'."\n";
+print OUT 'png(file="../Plots/CoverageBoxPlot.png", bg="white", width=240, height=480,type=c("cairo"))'."\n";
 print OUT 'boxplot(coverage,range=1.5,main="Target Region Coverage")'."\n";
 print OUT 'graphics.off()'."\n";
 close OUT;
@@ -274,7 +274,7 @@
 print OUT '  }'."\n";
 print OUT '}'."\n";
 # open output image and create plot
-print OUT 'png(file="../Plots/CoverageNtPlot.png", bg="white", width=540, height=480)'."\n";
+print OUT 'png(file="../Plots/CoverageNtPlot.png", bg="white", width=540, height=480,type=c("cairo"))'."\n";
 print OUT 'par(xaxs="i",yaxs="i")'."\n";
 print OUT 'plot(values$cov,values$count,ylim=c(0,100),pch=".",main="Cumulative Normalised Base-Coverage Plot",xlab="Normalizalised Coverage",ylab="Cumulative Nr. Of Bases")'."\n";
 print OUT 'lines(values$cov,values$count)'."\n";
@@ -423,7 +423,7 @@
 			}
 			my $width = 480 * $scale;
 			my $height = 240 * $scale;
-			print OUT 'png(file="../Plots/Coverage_'.$currgroup.'.png", bg="white", width='.$width.', height='.$height.')'."\n";
+			print OUT 'png(file="../Plots/Coverage_'.$currgroup.'.png", bg="white", width='.$width.', height='.$height.',type=c("cairo"))'."\n";
 			print OUT 'ylim = c(0,max(max(log10(coverage),log10('.($thresh+20).'))))'."\n";
 			print OUT 'mp <- barplot(log10(coverage),col=colors,main="Exon Coverage for '.$currgroup.'",ylab="Log10(Coverage)",ylim=ylim)'."\n";
 			print OUT 'text(mp, log10(coverage) + '.(0.4/$scale).',format(coverage),xpd = TRUE,srt=90)'."\n";
@@ -465,7 +465,7 @@
 		}
 		my $width = 480 * $scale;
 		my $height = 240 * $scale;
-		print OUT 'png(file="../Plots/Coverage_'.$currgroup.'.png", bg="white", width='.$width.', height='.$height.')'."\n";
+		print OUT 'png(file="../Plots/Coverage_'.$currgroup.'.png", bg="white", width='.$width.', height='.$height.',type=c("cairo"))'."\n";
 		print OUT 'ylim = c(0,max(max(log10(coverage),log10('.($thresh+20).'))))'."\n";
 		print OUT 'mp <- barplot(log10(coverage),col=colors,main="Exon Coverage for '.$currgroup.'",ylab="Log10(Coverage)", ylim=ylim)'."\n";
 		print OUT 'text(mp, log10(coverage) + log10(2),format(coverage),xpd = TRUE,srt=90)'."\n";
@@ -561,7 +561,7 @@
 		$exonstr =~ s/\s/_/g;
 		$exon =~ s/_/ /g;
 		$exon =~ s/\|/ /g;
-		print OUT 'png(file="../Plots/Coverage_'.$exonstr.'.png", bg="white", width='.$width.', height='.$height.')'."\n";
+		print OUT 'png(file="../Plots/Coverage_'.$exonstr.'.png", bg="white", width='.$width.', height='.$height.',type=c("cairo"))'."\n";
 		print OUT 'ylim = c(0,log10(max(max(coverage),'.($thresh+10).')))'."\n";
 		if ($orient eq '-') {
 			print OUT 'plot(positions,log10(coverage),type="n",main="Coverage for '.$exon.'",ylab="log10(Coverage)",ylim=ylim,xlab="Position",xlim=rev(range(positions)),sub="(Transcribed from minus strand)")'."\n";
@@ -658,7 +658,7 @@
 		$exonstr =~ s/\s/_/g;
 		$exon =~ s/_/ /g;
 		$exon =~ s/\|/ /g;
-		print OUT 'png(file="../Plots/Coverage_'.$exonstr.'.png", bg="white", width='.$width.', height='.$height.')'."\n";
+		print OUT 'png(file="../Plots/Coverage_'.$exonstr.'.png", bg="white", width='.$width.', height='.$height.',type=c("cairo"))'."\n";
 		print OUT 'ylim = c(0,log10(max(max(coverage),'.($thresh+10).')))'."\n";
 		if ($orient eq '-') {
 			print OUT 'plot(positions,log10(coverage),type="n",main="Coverage for '.$exon.'",ylab="log10(Coverage)",ylim=ylim,xlab="Position",xlim=rev(range(positions)),sub="(Transcribed from minus strand)")'."\n";