HighlightTrack-class: HighlightTrack class and methods

Description

A container for other track objects from the Gviz package that allows for the addition of a common highlighting area across tracks.

Usage

HighlightTrack(trackList=list(), range=NULL, start=NULL, end=NULL, width=NULL, chromosome, genome,
                           name="HighlightTrack",  ...)

Arguments

trackList

A list of Gviz track objects that all have to inherit from class GdObject.

range

An optional meta argument to handle the different input types. If the range argument is missing, all the relevant information to create the object has to be provided as individual function arguments (see below).

The different input options for range are:

[object Object],[object Object],[object Object]

start, end

An integer scalar with the genomic start or end coordinates for the highlighting range. Can also be supplied as part of the range argument.

width

An integer vector of widths for highlighting ranges. This can be used instead of either start or end to specify the range coordinates.

chromosome

The chromosome on which the track's genomic ranges are defined. A valid UCSC chromosome identifier if options(ucscChromosomeNames=TRUE). Please note that in this case only syntactic checking takes place, i.e., the argument value needs to be an integer, numeric character or a character of the form chrx, where x may be any possible string. The user has to make sure that the respective chromosome is indeed defined for the the track's genome. If not provided here, the constructor will try to build the chromosome information based on the available inputs, and as a last resort will fall back to the value chrNA. Please note that by definition all objects in the Gviz package can only have a single active chromosome at a time (although internally the information for more than one chromosome may be present), and the user has to call the chromosome<- replacement method in order to change to a different active chromosome.

genome

The genome on which the track's ranges are defined. Usually this is a valid UCSC genome identifier, however this is not being formally checked at this point. If not provided here the constructor will try to extract this information from the provided inputs, and eventually will fall back to the default value of NA.

name

Character scalar of the track's name. This is not really used and only exists fro completeness.

...

All additional parameters are ignored.

Objects from the Class

Objects can be created using the constructor function HighlightTrack.

Extends

Class "RangeTrack", directly.

Class "GdObject", by class "RangeTrack", distance 2.

Details

A track to conceptionally group other Gviz track objects into a meta track for the sole purpose of overlaying all the contained tracks with the same highlighting region as defined by the objects genomic ranges. During rendering the contained tracks will be treated as if they had been provided to the plotTracks function as individual objects.