heatmapByChromosome: heatmap with chromosome location as x axis
In methyAnalysis: DNA methylation data analysis and visualization

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

heatmap with chromosome location as x axis and plot together with other gene annotation information

heatmapByChromosome(genoSet, gene, annotationTracks = NULL, otherTrackList = NULL, phenoData = NULL,  
	phonoColorMap = NULL, extendRange = c(2000, 2000), includeGeneBody = TRUE, showFullModel = FALSE, sortSample = TRUE,  
	cytobandInfo = NULL, CpGInfo = NULL, genomeAxis = TRUE, dataTrackName = "Methylation Profile", lib = "org.Hs.eg.db", 
	genome = "hg19", genomicFeature = "TxDb.Hsapiens.UCSC.hg19.knownGene", gradient = c("blue", "white", "red"), 
	ncolor = 16, ylim = NULL, th = 0.99, main = "", selSample = NULL, ...)

`genoSet`	a GenoSet object keeping the methylation data as the "exprs" numeric matrix in the AssayData
`gene`	a Entrez Gene ID, or a GRanges object to define the chromosome range of the plot.
`annotationTracks`	A annotation tracks list returned by buildAnnotationTracks
`otherTrackList`	A list of other tracks supported by plotTracks function
`phenoData`	a data matrix with the same number of rows or columns as the columns of genoSet.
`phonoColorMap`	the colormap for expression heatmap
`extendRange`	extended range on each side of the gene
`includeGeneBody`	whether to include genebody of the provided gene
`showFullModel`	whether to show full gene model track when includeGeneBody = FALSE
`sortSample`	whether to sort samples or not
`cytobandInfo`	cytoband information
`CpGInfo`	CpG-island information, GRanges or bed file are supported
`genomeAxis`	whether to add genome axis or not
`dataTrackName`	the title of the data track
`lib`	the Entrez annotation library
`genome`	genome name
`genomicFeature`	genomic features: "TxDb" library or object, "Mart" object
`gradient`	the gradient color used by data track heatmap
`ncolor`	the number of color levels
`ylim`	the range for plotting the data.
`th`	the quantile threshold used to remove outlier, which affects the plot color ranges.
`main`	the title of the plot
`selSample`	subset of samples for plotting. It is designed for BigMatrix, which have to extract the data at the last moment.
`...`	other parameters used by `plotTracksWithDataTrackInfo`

This function plots heatmap with chromosome location as x axis and together with other gene annotation information. It is adapted based on the plotTracks function in Gviz package. Users can also provide a GRanges object to specify a plot region.

returns the grid viewport layout information

Pan Du

plotTracks, plotTracksWithDataTrackInfo, plotMethylationHeatmapByGene

	data(exampleMethyGenoSet)
	if (require(TxDb.Hsapiens.UCSC.hg19.knownGene) && require(Gviz)) {
		## define data track
		exampleMethyGenoSet <- checkChrName(exampleMethyGenoSet)

		## build annotation tracks
		selGene <- '1826'
		annotationTracks <- buildAnnotationTracks(selGene, includeGeneBody = FALSE, genomicFeature = "TxDb.Hsapiens.UCSC.hg19.knownGene", cytobandInfo=NA, CpGInfo=NA)
		heatmapByChromosome(exampleMethyGenoSet, selGene, annotationTracks = annotationTracks)
	}