plotGenomicAnnot {transcriptR} | R Documentation

## plotGenomicAnnot

### Description

Visualize genomic distribution of ChIP-seq peaks.

### Usage

    plotGenomicAnnot(object, plot.type = c("distrib", "enrich"), xlab, ylab,
      color)

    ## S4 method for signature 'ChipDataSet'
    plotGenomicAnnot(object, plot.type = c("distrib",
      "enrich"), xlab, ylab, color)

### Arguments

`object` | A `ChipDataSet` object.
`plot.type` | `Character`. One of ("distrib", "enrich"). Default: "enrich".
`xlab` | `Character`. Title of the x-axis.
`ylab` | `Character`. Title of the y-axis.
`color` | A character vector of length four, specifying colors for distinct genomic features (TSSs, exons, introns, intergenic regions).

### Details

Genomic distribution of the peaks can be visualized in two ways, either by observing the total number of peaks overlapping given genomic feature or by looking at the enrichment levels.

### Value

ggplot2 object.

### Author(s)

Armen R. Karapetyan

### See Also

`constructCDS`

### Examples

    ### Load ChipDataSet object
    data(cds)

    ### Plot the total number of peaks overlapping distinct genomic features
    plotGenomicAnnot(object = cds, plot.type = "distrib")

    ### Plot enrichment of the peaks at a given genomic feature (e.g. TSS)
    plotGenomicAnnot(object = cds, plot.type = "enrich")

[Package transcriptR version 1.12.0 Index]