chrHeatMap: Plot ChrStrandMatrix objects as heat maps along a chromosome

Description

Plots a either one or two ChrStrandMatrix objects (typically constructed using the createChrMatrix function) as heat maps along a specified chromosome, optionally clustering samples and including an idiogram.

Usage

chrHeatMap (strand.data, cytopaint.func=NULL, col = "heat.colors", start, end, breaks, RowSideColors, title=TRUE, margins = c(6, 6), cexCyto = 0.8, srtCyto=90, lmat = NULL, lhei = NULL, lwid = NULL, ...)

Arguments

strand.data

A ChrStrandMatrix object, or a list of such objects, one per strand to be plotted (or a single matrix for `both' strands), created using the createChrMatrix function.

cytopaint.func

A function closure taking a single argument, `boxwidth', and plotting its enclosed idiogram data at that width. See plotChrMap for the code used to generate this closure.

col

A vector of colors to use for the heat map, or the name of a function generating such a vector.

start

The starting genome coordinate for the plot.

end

The ending genome coordinate for the plot.

breaks

A vector of numeric break points indicating the boundaries between the col colors.

RowSideColors

A vector of colors to use for a color band indicating e.g. sample categories.

title

If TRUE, this causes the function to include default heat map subtitles indicating which chromosome and strand has been plotted. If FALSE or NULL, subtitles will left blank. If this argument is set to a character vector of the same length and order as strand.data its contents will be used as heat map subtitles.

margins

A numeric vector indicating the c(bottom, left) margins of the plot containing X and Y axes labels.

cexCyto

A positive number used to control the font size for the idiogram plot. For plots spanning just a few cytobands it may be worth setting this to a larger number, and srtCyto, below, to zero.

srtCyto

A number indicating the degree to which the idiogram text labels should be rotated. This defaults to 90 degrees, but for more detailed plots a setting of zero here often looks better.

lmat

An optional matrix to be passed to layout.

lhei

An optional vector of layout row heights.

lwid

An optional vector of layout row widths.

...

Additional arguments are passed to the drawMapDendro function.

Value

This function is executed for its side effects.

Details

Typically this function should not be called directly, but rather via the wrapper plotChrMap function. This function uses cytoband data from the UCSC genome annotation database and code adapted from the quantsmooth package to draw an idiogram of the chromosome, or a subset thereof.

References

lodplot and quantsmooth packages

Examples

Run this code

data('demo')
stranddata <- createChrMatrix( chrdata, chr=22, strand='forward', start=21925000, end=24300000 )
chrHeatMap(stranddata)

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