# HG changeset patch
# User stef
# Date 1407311909 14400
# Node ID 8434589e692c478339e0ade627dbd391cab0b80d
# Parent  8faab720c772d7d5a172c086ebb3085401f98c42
Uploaded

diff -r 8faab720c772 -r 8434589e692c QDNAseq.R
--- a/QDNAseq.R	Tue Aug 05 05:11:27 2014 -0400
+++ b/QDNAseq.R	Wed Aug 06 03:58:29 2014 -0400
@@ -156,6 +156,7 @@
 CSS_FILE  <- paste( TOOL_PATH, '/QDNAseq.css', sep="" )
 DECIMALS  <- 3
 WEB_LINK  <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html'
+PAR_SET   <- list( pch=19 )
 
 catMsg( "Starting QDNAseq wrapper" )	
 catMsg( "Loading R libraries" )
@@ -299,12 +300,14 @@
 plotted_images <- list() # to keep track of images for later linking
 regions <- list() # will contain the (called) segments
 
-png( noiseImgPath, width=PLOT_HEIGHT, height=PLOT_HEIGHT, res=PLOT_RES ); 
+png( noiseImgPath, width=PLOT_HEIGHT, height=PLOT_HEIGHT, res=PLOT_RES );
+	par( PAR_SET )
 	noisePlot( readCountsFiltered, col="darkgreen" )
 dev.off()
 
 if ( doCall ){
 	png( freqImgPath, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES ); 
+		par( PAR_SET )
 		frequencyPlot( copyNumbersCalled )
 	dev.off()	
 }
@@ -320,6 +323,7 @@
 	img_file <- paste( sample, '_', binSize, 'kbp_QDNAseq', type, '.png',  sep='')
 	img_file_path <- paste( outputPath, '/', img_file, sep='' )
 	png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES ); 
+		par( PAR_SET )
 		plot( copyNumbersSmooth[ ,sample ] ); 
 	dev.off()
 	plotted_images[[ sample ]][[ type ]] <- img_file
@@ -329,6 +333,7 @@
 		img_file <- paste( sample, '_', binSize, 'kbp_QDNAseq', type, '.png',  sep='')
 		img_file_path <- paste( outputPath, '/', img_file, sep='' )
 		png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES ); 
+			par( PAR_SET )
 			plot( copyNumbersCalled[ ,sample ] ); 
 		dev.off()
 		plotted_images[[ sample ]][[ type ]] <- img_file