Mercurial > repos > stef > qdnaseq
diff QDNAseq-plot.R @ 87:8391cdb7479c draft
Uploaded
| author | stef |
|---|---|
| date | Thu, 28 May 2015 14:19:57 -0400 |
| parents | 5eec30e0fcce |
| children | d2ea2b842c21 |
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--- a/QDNAseq-plot.R Thu May 28 14:19:49 2015 -0400 +++ b/QDNAseq-plot.R Thu May 28 14:19:57 2015 -0400 @@ -47,14 +47,17 @@ sample <- SAMPLE_INDEX png( outputPngPath, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES ) par( PAR_SET ) + ylab_text <- "log2 read counts" if ( whatToPlot == 'everything' ){ catMsg( c( "Plotting all data in object" ) ) - plot( qdnaseqObject[ ,sample ] ) + plot( qdnaseqObject[ ,sample ], ylab=ylab_text ) + abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" ) } else if( whatToPlot == 'chromosomes' ){ catMsg( c( "Plotting subset of chromosomes" ) ) fdata <- qdnaseqObject@featureData@data idx_region <- which( fdata$chromosome %in% chromosomesToPlot ) - plot( qdnaseqObject[ idx_region, sample ] ) + plot( qdnaseqObject[ idx_region, sample ], ylab=ylab_text ) + abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" ) } else if( whatToPlot == 'region' ){ regionC <- chrName regionS <- chrStart @@ -64,11 +67,12 @@ fdata <- qdnaseqObject@featureData@data idx_region <- which( fdata$chromosome == regionC & fdata$start > regionS & fdata$end < regionE ) + cat( idx_region, "\n") - plot( qdnaseqObject[ idx_region, sample ], doCalls=FALSE ) + plot( qdnaseqObject[ idx_region, sample ], doCalls=FALSE, ylab=ylab_text ) } #mtext( "plotted in galaxy", 3 ) - abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" ) + dev.off()