heatmapByChromosome {methyAnalysis} | R Documentation

## 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`

### 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.

### Value

returns the grid viewport layout information

### Author(s)

Pan Du

### 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)
    	}

[Package methyAnalysis version 1.22.0 Index]