comparison CoverageReport.pl @ 12:86df3f847a72 draft

Switched to R 3.0.2 from iuc, and moved bedtools to seperate tool_definition

11:2936bcb2a378

print OUT 'coverage <- coverage[,'.$covcol.']'."\n";
print OUT 'png(file="../Plots/CoverageBoxPlot.png", bg="white", width=240, height=480)'."\n";
print OUT 'boxplot(coverage,range=1.5,main="Target Region Coverage")'."\n";
print OUT 'graphics.off()'."\n";
close OUT;
system("cd $wd/Rout && /usr/bin/Rscript boxplot.R");

## global nt coverage plot
## use perl to make histogram (lower memory)
open IN, "$wd/Targets.Position.Coverage";
my %dens;

print OUT 'text(1,82,pos=2,col="red",labels=paste("%Bases: ",round(frac.y,2),"%",sep=""))'."\n";

print OUT 'graphics.off()'."\n";

close OUT;
system("cd $wd/Rout && /usr/bin/Rscript ntplot.R");
## PRINT TO .TEX FILE
open OUT, ">>$wd/Report/Report.tex";
# average coverage overviews
print OUT '\subsection*{Overall Summary}'."\n";
print OUT '{\small ';

			print OUT 'text(mp, log10(coverage) + '.(0.4/$scale).',format(coverage),xpd = TRUE,srt=90)'."\n";
			print OUT 'text(mp,par("usr")[3]-0.05,labels=entries,srt=45,adj=1,xpd=TRUE)'."\n";
			print OUT 'abline(h=log10('.$thresh.'),lwd=4,col=rgb(255,0,0,100,maxColorValue=255))'."\n";
			print OUT 'graphics.off()'."\n";
			close OUT;
			system("cd $wd/Rout && /usr/bin/Rscript barplot.R");
			if ($scale == 1) {
				push(@small,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');
			}
			else {
				push(@large,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');

		print OUT 'text(mp, log10(coverage) + log10(2),format(coverage),xpd = TRUE,srt=90)'."\n";
		print OUT 'text(mp,par("usr")[3]-0.1,labels=entries,srt=45,adj=1,xpd=TRUE)'."\n";
		print OUT 'abline(h=log10('.$thresh.'),lwd=4,col=rgb(255,0,0,100,maxColorValue=255))'."\n";
		print OUT 'graphics.off()'."\n";
		close OUT;
		system("cd $wd/Rout && /usr/bin/Rscript barplot.R");
		if ($scale == 1) {
			push(@small,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');
		}
		else {
			push(@large,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');

		print OUT 'failedcov <- coverage[coverage<'.$thresh.']'."\n";
		print OUT 'points(failedpos,log10(failedcov),col="red",pch=19)'."\n";
		print OUT 'graphics.off()'."\n";
		close OUT;
		# run R script
		system("cd $wd/Rout && /usr/bin/Rscript exonplot.R");
		# Add to .TEX
		print TEX '\begin{minipage}{0.5\linewidth}\centering'."\n";
		print TEX '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$exonstr.'.png}'."\n";
		print TEX '\end{minipage}'."\n";
		$col++;

		print OUT 'failedcov <- coverage[coverage<'.$thresh.']'."\n";
		print OUT 'points(failedpos,log10(failedcov),col="red",pch=19)'."\n";
		print OUT 'graphics.off()'."\n";
		close OUT;
		# run R script
		system("cd $wd/Rout && /usr/bin/Rscript exonplot.R");
		# Add to .TEX
		print TEX '\begin{minipage}{0.5\linewidth}\centering'."\n";
		print TEX '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$exonstr.'.png}'."\n";
		print TEX '\end{minipage}'."\n";
		$col++;

12:86df3f847a72

print OUT 'coverage <- coverage[,'.$covcol.']'."\n";
print OUT 'png(file="../Plots/CoverageBoxPlot.png", bg="white", width=240, height=480)'."\n";
print OUT 'boxplot(coverage,range=1.5,main="Target Region Coverage")'."\n";
print OUT 'graphics.off()'."\n";
close OUT;
system("cd $wd/Rout && Rscript boxplot.R");

## global nt coverage plot
## use perl to make histogram (lower memory)
open IN, "$wd/Targets.Position.Coverage";
my %dens;

print OUT 'text(1,82,pos=2,col="red",labels=paste("%Bases: ",round(frac.y,2),"%",sep=""))'."\n";

print OUT 'graphics.off()'."\n";

close OUT;
system("cd $wd/Rout && Rscript ntplot.R");
## PRINT TO .TEX FILE
open OUT, ">>$wd/Report/Report.tex";
# average coverage overviews
print OUT '\subsection*{Overall Summary}'."\n";
print OUT '{\small ';

			print OUT 'text(mp, log10(coverage) + '.(0.4/$scale).',format(coverage),xpd = TRUE,srt=90)'."\n";
			print OUT 'text(mp,par("usr")[3]-0.05,labels=entries,srt=45,adj=1,xpd=TRUE)'."\n";
			print OUT 'abline(h=log10('.$thresh.'),lwd=4,col=rgb(255,0,0,100,maxColorValue=255))'."\n";
			print OUT 'graphics.off()'."\n";
			close OUT;
			system("cd $wd/Rout && Rscript barplot.R");
			if ($scale == 1) {
				push(@small,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');
			}
			else {
				push(@large,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');

		print OUT 'text(mp, log10(coverage) + log10(2),format(coverage),xpd = TRUE,srt=90)'."\n";
		print OUT 'text(mp,par("usr")[3]-0.1,labels=entries,srt=45,adj=1,xpd=TRUE)'."\n";
		print OUT 'abline(h=log10('.$thresh.'),lwd=4,col=rgb(255,0,0,100,maxColorValue=255))'."\n";
		print OUT 'graphics.off()'."\n";
		close OUT;
		system("cd $wd/Rout && Rscript barplot.R");
		if ($scale == 1) {
			push(@small,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');
		}
		else {
			push(@large,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');

		print OUT 'failedcov <- coverage[coverage<'.$thresh.']'."\n";
		print OUT 'points(failedpos,log10(failedcov),col="red",pch=19)'."\n";
		print OUT 'graphics.off()'."\n";
		close OUT;
		# run R script
		system("cd $wd/Rout && Rscript exonplot.R");
		# Add to .TEX
		print TEX '\begin{minipage}{0.5\linewidth}\centering'."\n";
		print TEX '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$exonstr.'.png}'."\n";
		print TEX '\end{minipage}'."\n";
		$col++;

		print OUT 'failedcov <- coverage[coverage<'.$thresh.']'."\n";
		print OUT 'points(failedpos,log10(failedcov),col="red",pch=19)'."\n";
		print OUT 'graphics.off()'."\n";
		close OUT;
		# run R script
		system("cd $wd/Rout && Rscript exonplot.R");
		# Add to .TEX
		print TEX '\begin{minipage}{0.5\linewidth}\centering'."\n";
		print TEX '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$exonstr.'.png}'."\n";
		print TEX '\end{minipage}'."\n";
		$col++;