plotAlongChromLegend {tilingArray} | R Documentation

## Plot a legend for genomic features

### Description

Plot a legend for genomic features

### Usage

    plotAlongChromLegend(vpr, nr=2,
        featureColorScheme=1,
        featureExclude=c("chromosome", "nucleotide_match", "insertion"),
        mainLegend, cexLegend=0.35, cexMain=1)

### Arguments

`vpr` | vector specifying where to place the legend in figure (set up by using the `viewport` function from the grid package. When this function is called directly by the user this argument should be left missing.
`nr` | numeric scalar, specifying the number of rows to plot legend over (default value is 2).
`featureColorScheme` | numeric scalar, used to select a color scheme for the boxes representing genomic features such as coding sequences, ncRNAs etc. Currently the only value supported is 1.
`featureExclude` | character vector of names of feature types (in `gff`) that should not be plotted. Default is `"chromosome"`, `"nucleotide_match"` and `"insertion"`. Additional possible candidates include: `"ARS"`, `"repeat\_region"`, `"repeat\_family"` and `"nc\_primary\_transcript"`.
`mainLegend` | character vector specifying legend title.
`cexLegend` | numeric scalar specifying the magnification to be used for the legend text relative to the current text size.
`cexMain` | numeric scalar specifying the magnification to be used for the legend title relative to the current text size.

### Details

This function is usually called by `plotAlongChrom` when `doLegend` is TRUE. It can also be called directly by the user to produce a separate legend.

The following features are included in the legend (unless excluded using the `featuredExclude` option): `"chromosome"`, `"nucleotide_match"`, `"pseudogene"`, `"uORF"`, `"nc_primary_transcript"`, `"region"`, `"repeat_family"`, `"repeat_region"`, `"transposable_element"`, `"transposable_element_gene"`, `"ARS"`, `"centromere"`, `"telomere"`, `"insertion"`, `"CDS"`, `"CDS_dubious"`, `"ncRNA"`, `"tRNA"`, `"snRNA"`, `"rRNA"`, `"snoRNA"`, `"binding_site"` and `"TF_binding_site"`.

### Author(s)

Wolfgang Huber <huber@ebi.ac.uk>

### Examples

    ## plotAlongChromLegend(mainLegend="Legend")

[Package tilingArray version 1.22.0 Index]