heatmapByChromosome {methyAnalysis} | R Documentation |
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 |
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) }