plotWindow {ChIPseqR} | R Documentation

## Plot read counts within a genomic region

### Description

Read count within a selected region of the genome are plotted, optionally together with binding site score and location of predicted binding sites.

### Usage

    .plotWindow(data, chr, center, score, width=2000, bind, start, end, bind.col=3, score.type='l',
    	xlab=NULL, ylab="Read count", cutoff=TRUE, offset = 1, ...)

### Arguments

`data` | Object of class `ReadCounts` or a list of read counts.
`chr` | A character string or numeric index identifying the the chromosome on which the region is located.
`center` | Numeric value giving the center of the region on chromosome `'chr'` that should be plotted.
`score` | An object of class `BindScore`, may be missing.
`width` | Width of the window to plot. The plotted region will be [center - width/2, center + width/2].
`bind` | Length of binding site, ignored if `'score'` is missing.
`start` | Start of plotting window (may be used together with `end` instead of `center`).
`end` | End of plotting window (may be used together with `start` instead of `center`).
`bind.col` | Color used to indicate location of binding sites, ignored if `'score'` is missing.
`score.type` | Plotting type to use for score, ignored if `'score'` is missing.
`xlab` | X-axis label. This defaults to a description of the genomic location constructed from `'chr'`, `'center'` and `'width'`
`ylab` | Y-axis label.
`cutoff` | Logical indicating whether the significance threshold used to predict binding site locations should be indicated by a horizontal line in the plot.
`offset` | Position on chromosome `chr` corresponding to the first read count in `data`.
`...` | Further arguments to `plot`.

### Details

If `'score'` is present the binding site score is plotted on top of read counts. Scores are rescaled to lie between 0 and the maximum number of reads in the window. A corresponding scale is added to the right hand axis.

### Value

Called for its side effect.

### Author(s)

Peter Humburg

[Package ChIPseqR version 1.48.0 Index]