plot,ReadCounts,missing-method {ChIPseqR} | R Documentation

## Diagnostic Plots for Read Counts

### Description

Produces plots to assess the distribution of reads, either for an entire chromosome or within a (small) window.

### Usage

    ## S4 method for signature 'ReadCounts,missing'
    plot(x, chr, center, score, width=2000, type=c("hilbert", "window"), ...)
    ## S4 method for signature 'RLEReadCounts,missing'
    plot(x, chr, center, score, width=2000, type=c("hilbert", "window"), ...)

### Arguments

`x` | Object of class `ReadCounts` or `RLEReadCounts`.
`chr` | Index or name of chromosome for which read counts should be plotted.
`center` | For type ‘window’, the center coordinate of the window to plot.
`score` | For type ‘window’, an object of type `BindScore` (or `BindScore`) that should be used to include information about the score and predicted binding sites into the plot.
`width` | For type ‘window’, the width of the window.
`type` | Character string indicating the type of plot that should be produced (see details).
`...` | Further arguments (see details).

### Details

Type ‘window’ produces a plot that shows read counts as vertical bars. If `score` is not missing, it is used to plot the score and predicted binding sites (if any) as well. Any additional arguments are passed on to `.plotWindow`.

Type ‘hilbert’ produces a Hilbert curve plot of read counts for an entire chromosome. Additional arguments are passed on to `.plotReads`.

### Value

Called for its side effect.

### Author(s)

Peter Humburg

### See Also

`hilbertImage`

[Package ChIPseqR version 1.44.0 Index]