Mercurial > repos > geert-vandeweyer > coverage_report

changeset 22:95062840f80f draft

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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 06ccf2048b8f
children a718420c834e
files CoverageReport.pl
diffstat 1 files changed, 6 insertions(+), 6 deletions(-) [+]
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";