recoupHeatmap {recoup} | R Documentation

## Plot genomic coverage heatmaps

### Description

This function takes as input argument and output object from `recoup` and creates heatmaps depicting genomic coverages using the `ComplexHeatmap` package and the options present in the input object. It can be used with saved recoup outputs so as to recreate the plots without re-reading BAM/BED files and re-calculating coverages.

### Usage

        recoupHeatmap(recoupObj, samples = NULL, rc = NULL)

### Arguments

`recoupObj` | a list object created from `recoup`.
`samples` | which samples to plot. Either numeric (denoting the sample indices) or sample ids. Defaults to `NULL` for all samples.
`rc` | fraction (0-1) of cores to use in a multicore system. It defaults to `NULL` (no parallelization).

### Value

The function returns the `recoupObj` with the slot for the profile plot filled. See also the `recoupPlot`, `getr` and `setr` function.

### Author(s)

Panagiotis Moulos

### Examples

    # Load some data
    data("recoup_test_data",package="recoup")

    # Calculate coverages
    test.tss <- recoup(
        test.input,
        design=NULL,
        region="tss",
        type="chipseq",
        genome=test.genome,
        flank=c(2000,2000),
        selector=NULL,
        plotParams=list(profile=FALSE,heatmap=FALSE),
        rc=0.5
    )

    # Plot coverage profiles
    recoupHeatmap(test.tss,rc=0.5)

[Package recoup version 1.15.1 Index]