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Compacting pdfs when running under R 2.13+.

This commit is contained in:
Khalid Shakir 2011-10-27 14:51:56 -04:00
parent b80d407dc7
commit 4d0e34109f
3 changed files with 33 additions and 0 deletions
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13
public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_OtherCovariate.R
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@ -1,5 +1,7 @@
#!/bin/env Rscript #!/bin/env Rscript
library(tools)
args <- commandArgs(TRUE) args <- commandArgs(TRUE)
verbose = TRUE verbose = TRUE
@ -47,6 +49,9 @@ if( is.numeric(c$Covariate) ) {
} }
dev.off() dev.off()
if (exists('compactPDF')) {
compactPDF(outfile)
}
# #
# Plot mean quality versus the covariate # Plot mean quality versus the covariate
@ -69,6 +74,10 @@ if( is.numeric(c$Covariate) ) {
} }
dev.off() dev.off()
if (exists('compactPDF')) {
compactPDF(outfile)
}
# #
# Plot histogram of the covariate # Plot histogram of the covariate
# #
@ -106,3 +115,7 @@ if( is.numeric(c$Covariate) ) {
axis(2,axTicks(2), format(axTicks(2), scientific=F)) axis(2,axTicks(2), format(axTicks(2), scientific=F))
} }
dev.off() dev.off()
if (exists('compactPDF')) {
compactPDF(outfile)
}

14
public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_QualityScoreCovariate.R
View File

@ -1,5 +1,7 @@
#!/bin/env Rscript #!/bin/env Rscript
library(tools)
args <- commandArgs(TRUE) args <- commandArgs(TRUE)
input = args[1] input = args[1]
@ -33,6 +35,10 @@ points(f$Qreported, f$Qempirical, type="p", col="maroon1", pch=16)
abline(0,1, lty=2) abline(0,1, lty=2)
dev.off() dev.off()
if (exists('compactPDF')) {
compactPDF(outfile)
}
# #
# Plot Q empirical histogram # 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)) axis(2,axTicks(2), format(axTicks(2), scientific=F))
dev.off() dev.off()
if (exists('compactPDF')) {
compactPDF(outfile)
}
# #
# Plot Q reported histogram # 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") points(hst2$f.Qreported, hst2$f.nBases, type="h", lwd=4, col="maroon1")
axis(2,axTicks(2), format(axTicks(2), scientific=F)) axis(2,axTicks(2), format(axTicks(2), scientific=F))
dev.off() dev.off()
if (exists('compactPDF')) {
compactPDF(outfile)
}

6
public/R/scripts/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R
View File

@ -1,5 +1,7 @@
#!/bin/env Rscript #!/bin/env Rscript
library(tools)
args <- commandArgs(TRUE) args <- commandArgs(TRUE)
verbose = TRUE verbose = TRUE
@ -85,3 +87,7 @@ if ( ! is.null(sensitivity) ) {
} }
dev.off() dev.off()
if (exists('compactPDF')) {
compactPDF(outfile)
}