plotMethylationHeatmapByGene: plot methylation heatmap by genes

Description

plot methylation heatmap by genes

Usage

plotMethylationHeatmapByGene(selGene, methyGenoSet, gene2tx = NULL, expression.tx = NULL, expression.other = NULL, 
	phenoData = NULL, sortBy=c('expression', 'methylation', NA), scaledExpression = FALSE, labelPrefix.expression.other = '', 
	showAllTx = TRUE, useBetaValue = TRUE, includeGeneBody = FALSE, CpGInfo = NULL, genomicFeature = NULL,
	phenoColor = list(gradient=c("green", "black", "red")), th = 0.99, title.suffix = NULL, addLegend = TRUE,
	methylationLegendTitle = NULL, expressionLegendTitle = "Expression\n(log2-RPKM)", 
	gradient = c("blue", "white", "red"), ncolor = 16, main = NULL, newPlot = TRUE, selSample = NULL, ...)

Arguments

selGene

a vector of EntrezIDs or a list of gene2tx

methyGenoSet

a GenoSet object for methylation data

gene2tx

a gene to transcript mapping list, used for retrieving expression.tx data

expression.tx

an ExpressionSet or data matrix for transcript expression

expression.other

an ExpressionSet or data matrix for other types of expression, whose dimnames matches expression.tx

phenoData

a data.frame for phenoData information

sortBy

whether to sort samples based on the mean of expression profiles, methylation cluster or NA (no sorting)

scaledExpression

whether to scale the expression values based on maximum expression (to the range of 0 to 1)

labelPrefix.expression.other

the labelPrefix for the "expression.other" colnames

showAllTx

whether to show all transcript in gene2tx or just those provided in selGene

useBetaValue

whether to use methylation Beta-value in the plot.

includeGeneBody

if FALSE, then only shows the promoter region

CpGInfo

a bed file or GRanges for CpG island information

genomicFeature

used by buildAnnotationTracks function

phenoColor

a list of colors corresponding to phenoData

the quantile threshold used to remove outlier, which affects the plot color ranges.

title.suffix

a string attached to the end of the title

addLegend

whether to add a legend or not

methylationLegendTitle

title for methylation colorbar legend

expressionLegendTitle

title for expression colorbar legend

gradient

the gradient color to show the DataTrack

ncolor

the number of color levels

main

title of the plot. If it is null, then the Gene Symbol will be the plot title

newPlot

whether to create a new plot or add it to previous 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 heatmapByChromosome

Value

returns the grid viewport information

Details

Function, plotMethylationHeatmapByGene, is specifically designed for the methylation data. It plots one gene or genomic range each time. Users can add phenotypes or matched gene expression data to the right panel of the plot. Figure legends can be also added. By default, the plotMethylationHeatmapByGene plots methylation Beta-values (in the range of 0 to 1) instead of M-values. Users can set useBetaValue as FALSE if they want to change to M-values.

Examples

Run this code


data('exampleMethyGenoSet') 
if (require(TxDb.Hsapiens.UCSC.hg19.knownGene)) {
  genomicFeature <- 'TxDb.Hsapiens.UCSC.hg19.knownGene'
  selGene <- '1826'
  plotMethylationHeatmapByGene(selGene, methyGenoSet=exampleMethyGenoSet, phenoData=colData(exampleMethyGenoSet), genomicFeature=genomicFeature)

  ## use different color map for expression data
  es.example <- matrix(runif(ncol(exampleMethyGenoSet), max=10), nrow=1)
  rownames(es.example) <- selGene
  colnames(es.example) <- colnames(exampleMethyGenoSet)
  plotMethylationHeatmapByGene(selGene, methyGenoSet=exampleMethyGenoSet, expression.tx=es.example, genomicFeature=genomicFeature, phenoColor=list(gradient=c("green", "black", "red")))
}