plotHeatmap {copynumber} | R Documentation

## Plot copy number heatmap

### Description

Heatmap reflecting the magnitude of estimated copy numbers relative to some pre-defined limits. Estimates may be obtained using `pcf` or `multipcf`, and results may be visualized over the entire genome or by chromosomes.

### Usage

    plotHeatmap(segments, upper.lim, lower.lim = -upper.lim, pos.unit = "bp",
        chrom = NULL, layout = c(1, 1),...)

### Arguments

`segments` | a data frame containing the segmentation results found by either `pcf` or `multipcf`.
`upper.lim` | a positive numeric vector giving the upper limits(s) to be applied. The colors in the heatmap will reflect the magnitude of the estimated copy numbers relative to this limit, see details.
`lower.lim` | a negative numeric vector of same length as `upper.lim` giving the lower limits(s) to be applied. Default is to use the negative value of `upper.lim`.
`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 three giving the colors to interpolate in the heatmap, default is c("dodgerblue","black","red"). `n.col` an integer giving the number of color shades to be applied in the interpolation, default is 50. `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. Default is 0, which implies that there is no space. `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 segments are represented by a rectangle plotted in a color corresponding to the difference between the segment copy number value and the limits. If the value is below `lower.lim`, the color of the rectangle will equal the input in `colors[1]` (default dodgerblue). If the value is above `lower.lim`, but below zero, the color of the rectangle will be a nuance between the input in `colors[1]` and `colors[2]` (default black). The closer the value is to zero, the closer the nuance will be to `colors[2]`. Similary, if the value is above `upper.lim`, the color of the rectangle will equal the input in `colors[3]` (default red), whereas if the value is below `upper.lim`, but above zero, the color will be a nuance between the input in `colors[2]` and `colors[3]`. Again, the closer the value is to zero, the closer the nuance will be to `colors[2]`.

Each row in the heatmap 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)

    #Heatmap for entire genome, two limit values:
    plotHeatmap(segments=seg,upper.lim=c(0.1,0.5),layout=c(2,1))

    #Heatmap for the first 4 chromosomes:
    plotHeatmap(segments=seg,upper.lim=0.1,chrom=c(1:4),layout=c(2,2))

[Package copynumber version 1.28.0 Index]