plotAlongChromLegend: Plot a legend for genomic features
In tilingArray: Transcript mapping with high-density oligonucleotide tiling arrays

Description Usage Arguments Details Author(s) Examples

Plot a legend for genomic features

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

`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.

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".