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Last data update: 2014.03.03

R: heatmap with chromosome location as x axis

heatmapByChromosome

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

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)
	}

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(methyAnalysis)
Loading required package: grid
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in "GenomicRanges" for requests: overlapsAny
No methods found in "genoset" for requests: rowRanges, rowRanges<-, toGenomeOrder
Warning messages:
1: multiple methods tables found for 'colMeans' 
2: multiple methods tables found for 'colSums' 
3: multiple methods tables found for 'rowMeans' 
4: multiple methods tables found for 'rowSums' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/methyAnalysis/heatmapByChromosome.Rd_%03d_medium.png", width=480, height=480)
> ### Name: heatmapByChromosome
> ### Title: heatmap with chromosome location as x axis
> ### Aliases: heatmapByChromosome
> ### Keywords: methods hplot
> 
> ### ** 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)
+ 	}
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: GenomicFeatures
Loading required package: Gviz
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>