plotAberration {copynumber} | R Documentation

## Plot areas with copy number aberrations

### Description

Create plots reflecting the location of aberrated segments. Results may be visualized over the entire genome or by chromosomes.

### Usage

    plotAberration(segments, thres.gain, thres.loss = -thres.gain, pos.unit = "bp",
        chrom = NULL, layout = c(1, 1),...)

### Arguments

`segments` | a data frame containing the segmentation results found by either `pcf` or `multipcf`.
`thres.gain` | a numeric vector giving the threshold value(s) to be applied for calling gains.
`thres.loss` | a numeric vector of same length as `thres.gain` giving the threshold value(s) to be applied for calling losses. Default is to use the negative value of `thres.gain`.
`pos.unit` | the unit used to represent the probe positions. Allowed options are "mbp" (mega base pairs), "kbp" (kilo base pairs) or "bp" (base pairs). By default assumed to be "bp".
`chrom` | a numeric or character vector with chromosome number(s) to indicate which chromosome(s) is (are) to be plotted. If unspecified the whole genome is plotted.
`layout` | the vector of length two giving the number of rows and columns in the plot window. Default is `c(1,1)`.
`...` | other optional graphical parameters. These include the plot arguments `xlab`, `ylab`, `main`, `cex.main`, `mgp`, `cex.lab`, `cex.axis`, `mar` and `title` (see `par` on these), as well as `plot.size`, `plot.unit`, `plot.ideo`, `ideo.frac`, `cyto.text`, `assembly` and `cex.cytotext` (see `plotSample` on these). In addition, a range of graphical arguments specific for this plot function may be specified: `colors` a character vector of length two where the first and second element specifies the color used to represent loss and gain, respectively. Default is c("dodgerblue","red"). `sample.labels` a logical value indicating whether sample labels are to be plotted along the y-axis. Default is TRUE. `sep.samples` a number in the range 0 to 0.4 used to create some space between samples. 0 implies that there is no space. Default is 2/nsample, where nsample is the number of samples found in `segments`. `sample.line` a numeric scalar giving the margin line where the sample labels should be written, starting at 0 counting outwards. Default is 0.2. `sample.cex` the size of the sample labels.

### Details

For each sample, the aberrated regions are shown in the color specified in `colors[1]` (default dodgerblue) if the segment value is below `thres.loss` and the color specified in `colors[2]` (default red) if the segment value is above `thres.gain`. Non-aberrated regions are shown in white. Each row in the plot represents a sample, while probe positions are reflected along the x-axis.

### Note

This function applies `par(fig)`, and is therefore not compatible with other setups for arranging multiple plots in one device such as `par(mfrow,mfcol)`.

### Author(s)

Gro Nilsen

### Examples

    #Load lymphoma data
    data(lymphoma)

    #Run pcf to obtain estimated copy number values
    seg <- pcf(data=lymphoma,gamma=12)

    #Plot aberrations for the entire genome
    plotAberration(segments=seg,thres.gain=0.15)

    #Plot aberrations for the first 4 chromosomes:
    plotAberration(segments=seg,thres.gain=0.1,chrom=c(1:4),layout=c(2,2))

[Package copynumber version 1.28.0 Index]