plotAlongChromLegend: 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.

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".