CoverageHeatmap: Generate a Heatmap of coverage

In heatmaps: Flexible Heatmaps for Functional Genomics and Sequence Features

Description

Generate a Heatmap of coverage

Usage

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)

• windows = GenomicRanges,track = GenomicRanges: Heatmap of Coverage from 2 GRanges

• windows = GenomicRanges,track = RleList: Heatmap of Coverage from GRanges + RleList

Examples

data(HeatmapExamples)
CoverageHeatmap(windows, rle_list, coords=c(-100, 100), label="Example")

Example output

Attaching package: 'heatmaps'

The following object is masked from 'package:base':

    scale

coords: -100 100 
nseq: 200 
obs: 40000 
scale: 0 1 
label: Example 

heatmaps documentation built on Nov. 8, 2020, 7:32 p.m.