diff QDNAseq-plot.R @ 27:f89205f51e27 draft default tip

Uploaded

--- a/QDNAseq-plot.R	Mon Jul 06 05:38:44 2015 -0400
+++ b/QDNAseq-plot.R	Mon Jul 06 05:41:08 2015 -0400
@@ -37,13 +37,42 @@
 catMsg( c( rVersion ) )
 
 qdnaseqObject <- readRDS( rdsFilePath )
+chromosomesToPlot <- unlist( strsplit( chromosomesToPlotString, ",") )
+
+#cat( "CHROM: ", chromosomesToPlotString, "\n" )
+#cat( "REGION: ", regionToPlotString, "\n" )
+#cat( "What to plot: ", whatToPlot, "\n" )
+
 ## COPYNUMBER PLOT
 sample <- SAMPLE_INDEX
 png( outputPngPath, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES )
 	par( PAR_SET )
-	plot( qdnaseqObject[ ,sample ] ) 
+	ylab_text <- "log2 read counts"
+	if ( whatToPlot == 'everything' ){
+		catMsg( c( "Plotting all data in object" ) )
+		plot( qdnaseqObject[ ,sample ], ylab=ylab_text )
+		abline( h=c(-4,-3,-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$chromosome %in% chromosomesToPlot )
+		plot( qdnaseqObject[ idx_region, sample ], ylab=ylab_text )
+		abline( h=c(-4,-3,-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" )
+	} else if( whatToPlot == 'region' ){
+		regionC <- chrName
+		regionS <- chrStart
+		regionE <- chrEnd
+		if ( regionS > regionE ) stop("Chosen start is > end")
+		catMsg( c( "Plotting genomic region (chr=", regionC, " start=", regionS, " end=", regionE, ")" ) )
+		
+		fdata <- qdnaseqObject@featureData@data
+		idx_region <- which( fdata$chromosome == regionC & fdata$start > regionS & fdata$end < regionE )
+		cat( idx_region, "\n")
+		
+		plot( qdnaseqObject[ idx_region, sample ], doCalls=FALSE, 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()