Repository 'coverage_report'
hg clone https://toolshed.g2.bx.psu.edu/repos/geert-vandeweyer/coverage_report

Changeset 22:95062840f80f (2014-11-17)
Previous changeset 21:06ccf2048b8f (2014-11-06) Next changeset 23:a718420c834e (2015-02-12)
Commit message:
Correction to png calls to use cairo instead of x11. thanks to Eric Enns for pointing this out.
modified:
CoverageReport.pl
b
diff -r 06ccf2048b8f -r 95062840f80f CoverageReport.pl
--- 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";