plotTracksWithDataTrackInfo: plot Tracks with additional DataTrack information added to...
In methyAnalysis: DNA methylation data analysis and visualization

Description Usage Arguments Details Value Author(s) See Also Examples

plot Tracks with additional DataTrack information added to the left of the plot

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plotTracksWithDataTrackInfo(trackList, labels = NULL, grange2show = NULL, dataTrackName = NULL, dataInfo = NULL, dataColorMap = NULL,
	dataInfoRange = NULL, dataBackground = gray(0.9), minHeatmapColumnWidth = 2, labelWidth = 0.1, 
	gradient = c("blue", "white", "red"), ncolor = 16, main = "", newPlot = FALSE, sizes = NULL, ...)

`trackList`	a list of tracks supported by `plotTracks` function
`labels`	the sample labels. By default, it will use the rownames of dataTrack. It can also be a list if there are multiple dataTracks. And the list names should be consistent with dataTrack names. Providing a subset of dataTrack labels is allowed.
`grange2show`	a GRanges to indicate the plot range
`dataTrackName`	the name of the DataTrack
`dataInfo`	a data matrix or data.frame to show the related sample information, e.g. its expression profile
`dataColorMap`	the color map to plot the dataInfo
`dataInfoRange`	the range of dataInfo to control the range of color map
`dataBackground`	the background color for the data tracks
`minHeatmapColumnWidth`	the minimum width (points) of the heatmap data column
`labelWidth`	the width of the label, which is the ratio of the entire plot width
`gradient`	the gradient color to show the DataTrack
`ncolor`	the number of color levels
`main`	the title of the plot
`newPlot`	whether to create a new plot or add it to previous plot
`sizes`	the track sizes used by plotTracks function
`...`	other parameters used by plotTracks

This function is adapted based on the plotTracks function in Gviz package. It adds sample labels to the heatmap dataTracks.

Grid viewport layout information

Pan Du

See Also plotTracks, heatmapByChromosome

	data(exampleMethyGenoSet)
	if (require(TxDb.Hsapiens.UCSC.hg19.knownGene) && require(Gviz)) {
		## define data track
		exampleMethyGenoSet <- checkChrName(exampleMethyGenoSet)
		dTrack <- DataTrack(range=suppressWarnings(as(rowRanges(exampleMethyGenoSet), 'GRanges')), data=t(exprs(exampleMethyGenoSet)), 
			chromosome='chr21', type='heatmap')		

		## build annotation tracks
		annotationTracks <- buildAnnotationTracks('1826', includeGeneBody = FALSE, genomicFeature = "TxDb.Hsapiens.UCSC.hg19.knownGene", cytobandInfo=NA, CpGInfo=NA)
		trackList <- c(annotationTracks, list(dTrack))
		plotTracksWithDataTrackInfo(trackList, labels=colnames(exampleMethyGenoSet), grange2show = attr(annotationTracks, 'grange2show'))
	}