methyAnalysis (version 1.14.0)

heatmapByChromosome: heatmap with chromosome location as x axis

Description

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

Usage

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, ...)

Arguments

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

Value

returns the grid viewport layout information

Details

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.

See Also

plotTracks, plotTracksWithDataTrackInfo, plotMethylationHeatmapByGene

Examples

	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)
	}