plotChrMap: Plot data as an annotated heat map along a chromosome

Description

Given a ChrStrandData object (produced by the makeChrStrandData function), this function plots a heat map of its data values along a specified chromosome, optionally clustering samples and including an idiogram.

Usage

plotChrMap( data, chr, start = 1, end, subset = NULL, cytoband, interval = ceiling((end-start)/500), strands = c('forward', 'reverse'), ... )

Arguments

data

A ChrStrandData object, output from the makeChrStrandData function.

chr

Chromosomal id, chromosome to plot 1:22,X,Y.

start

Optional start chromosome position from which to commence plotting.

end

Optional end chromosome position.

subset

Optional numeric vector listing the samples from data to plot.

cytoband

Optional cytological band to plot (e.g. `q23').

interval

An optional interval size controlling the plot detail level.

strands

The chromosome strands to plot (a one- or two-element character vector, values `forward', `reverse', or `both').

...

Additional arguments are passed to the chrHeatMap function.

Value

A ChrMapPlot object containing a list of probe/gene identifiers mapped to their corresponding display locations, for use with grabChrMapProbes.

Details

This function is used to plot ChrStrandData objects (the output of the makeChrStrandData function) as heatmaps arranged along genome coordinates. The default heat map will plot the entire forward strand for the chosen chromosome at the top of the figure, with an idiogram and the reverse strand below it. To plot both strands overlaid, use the strands='both' argument. Probe or gene signals are averaged over a window size controlled by interval, such that the default length of each heat map segment is 1/500 the total heat map width. This can be varied as required to control the resolution of the plot. This function uses both the start and end chromosomal locations for each gene to plot heatmap positions, and as such will not work with older AnnotationDbi packages.

See the related functions from this package for further plotting arguments which may be passed to this function. In particular, see the drawMapDendro documentation for arguments used to control sample clustering and plot axis font sizes, and chrHeatMap for arguments relating to the idiogram plot. Note that the plotting area layout() and par() values are not reset on exit, so that grabChrMapProbes can be subsequently used on the output.

Idiogram plotting is currently only supported for data mapping to human, mouse and rat genomes. In principle this is extendable to any organism for which the UCSC genome browser includes cytoband information. Please contact the maintainer of this package for help in such cases.

References

annotate package

Examples

Run this code

data('demo')
plotChrMap(chrdata, '22', cytoband='q11', labRow=ALLs.chr22$mol.biol,
cexCol=0.8, cexCyto=1.2, srtCyto=0)

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