CoverageHeatmap: Generate a Heatmap of coverage

Description Usage Arguments Value Methods (by class) Examples

Description

Generate a Heatmap of coverage

Usage

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CoverageHeatmap(windows, track, ...)

## S4 method for signature 'GenomicRanges,GenomicRanges'
CoverageHeatmap(windows, track,
  coords = NULL, weight = 1, label = NULL, nbin = 0)

## S4 method for signature 'GenomicRanges,RleList'
CoverageHeatmap(windows, track,
  coords = NULL, label = NULL, nbin = 0)

Arguments

windows

A set of GRanges of equal length

track

A GRanges or RleList object specifying coverage

...

additional arguments used by methods

This function generates a Heatmap object from a set of windows and an object containing genome-wide information about coverage. Either a GRanges or an RleList can be used. In the former case, the "weight" paramter is passed directly to the 'coverage' function. If nbin is set, binned coverage is calculated which will save memory and time when plotting and average out varible data.

If the coverage track contains negative values, then the scale will be centered on zero, ie. c(-max(abs(image(hm))), max(abs(image(hm)))). This makes more sense for most color schemes which are centered on zero, and avoids misleading plots where either positive or negative values are over-emphasised. See ?getScale for details. The scale can be manually reset if desired using the "scale" method.

coords

Co-ordinates for the heatmap, defaults to c(0, width(windows))

weight

Passed to coverage(track) constructor if class(track) == "GRanges"

label

Label for the heatmap

nbin

If set, number of bins to use across each window

Value

A Heatmap object

Methods (by class)

Examples

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mgperry/heatmaps documentation built on May 22, 2019, 8:53 p.m.