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

Description

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

Usage

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, ...)

Arguments

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

Value

Grid viewport layout information

Details

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

Examples

Run this code


	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'))
	}