Mercurial > repos > stef > qdnaseq
changeset 53:8434589e692c draft
Uploaded
| author | stef |
|---|---|
| date | Wed, 06 Aug 2014 03:58:29 -0400 |
| parents | 8faab720c772 |
| children | 4ea771d6aa74 |
| files | QDNAseq.R |
| diffstat | 1 files changed, 6 insertions(+), 1 deletions(-) [+] |
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--- 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