CoverageHeatmap {heatmaps} | R Documentation

## Generate a Heatmap of coverage

### 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")

[Package heatmaps version 1.14.0 Index]