From 4d0e34109fbc61875a98d9ee9a27a0183c5fbb6d Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Thu, 27 Oct 2011 14:51:56 -0400
Subject: [PATCH] Compacting pdfs when running under R 2.13+.

---
 .../plot_residualError_OtherCovariate.R            | 13 +++++++++++++
 .../plot_residualError_QualityScoreCovariate.R     | 14 ++++++++++++++
 .../walkers/variantrecalibration/plot_Tranches.R   |  6 ++++++
 3 files changed, 33 insertions(+)

diff --git a/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_OtherCovariate.R b/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_OtherCovariate.R
index a1385ff3f..15c6fc8f0 100644
--- a/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_OtherCovariate.R
+++ b/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_OtherCovariate.R
@@ -1,5 +1,7 @@
 #!/bin/env Rscript
 
+library(tools)
+
 args <- commandArgs(TRUE)
 verbose = TRUE
 
@@ -47,6 +49,9 @@ if( is.numeric(c$Covariate) ) {
 }
 dev.off()
 
+if (exists('compactPDF')) {
+  compactPDF(outfile)
+}
 
 #
 # Plot mean quality versus the covariate
@@ -69,6 +74,10 @@ if( is.numeric(c$Covariate) ) {
 }
 dev.off()
 
+if (exists('compactPDF')) {
+  compactPDF(outfile)
+}
+
 #
 # Plot histogram of the covariate
 #
@@ -106,3 +115,7 @@ if( is.numeric(c$Covariate) ) {
 	axis(2,axTicks(2), format(axTicks(2), scientific=F))
 }
 dev.off()
+
+if (exists('compactPDF')) {
+  compactPDF(outfile)
+}
diff --git a/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_QualityScoreCovariate.R b/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_QualityScoreCovariate.R
index 81bc9460d..33eeb1f16 100644
--- a/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_QualityScoreCovariate.R
+++ b/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_QualityScoreCovariate.R
@@ -1,5 +1,7 @@
 #!/bin/env Rscript
 
+library(tools)
+
 args <- commandArgs(TRUE)
 
 input = args[1]
@@ -33,6 +35,10 @@ points(f$Qreported, f$Qempirical, type="p", col="maroon1", pch=16)
 abline(0,1, lty=2)
 dev.off()
 
+if (exists('compactPDF')) {
+  compactPDF(outfile)
+}
+
 #
 # Plot Q empirical histogram
 #
@@ -52,6 +58,10 @@ points(hst2$f.Qempirical, hst2$f.nBases, type="h", lwd=4, col="maroon1")
 axis(2,axTicks(2), format(axTicks(2), scientific=F))
 dev.off()
 
+if (exists('compactPDF')) {
+  compactPDF(outfile)
+}
+
 #
 # Plot Q reported histogram
 #
@@ -68,3 +78,7 @@ plot(hst$e.Qreported, hst$e.nBases, type="h", lwd=4, xlim=c(0,maxQ), ylim=c(0,yM
 points(hst2$f.Qreported, hst2$f.nBases, type="h", lwd=4, col="maroon1")
 axis(2,axTicks(2), format(axTicks(2), scientific=F))
 dev.off()
+
+if (exists('compactPDF')) {
+  compactPDF(outfile)
+}
diff --git a/public/R/scripts/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R b/public/R/scripts/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R
index a79ddd3ab..d96add768 100755
--- a/public/R/scripts/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R
+++ b/public/R/scripts/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R
@@ -1,5 +1,7 @@
 #!/bin/env Rscript
 
+library(tools)
+
 args <- commandArgs(TRUE)
 verbose = TRUE
 
@@ -85,3 +87,7 @@ if ( ! is.null(sensitivity) ) {
 }
 
 dev.off()
+
+if (exists('compactPDF')) {
+  compactPDF(outfile)
+}