ReferenceTrack-class: ReferenceTrack class and methods

In ivanek/Gviz: Plotting data and annotation information along genomic coordinates

ReferenceTrack class and methods

Description

A class allow for on-demand streaming of data off the file system.

Usage

availableDefaultMapping(file, trackType)

## S4 method for signature 'ReferenceTrack'
initialize(
  .Object,
  stream,
  reference,
  mapping = list(),
  args = list(),
  defaults = list()
)

Arguments

file	A character scalar with a file name or just a file extension.
trackType	A character scalar with one of the available track types in the package.
.Object	.Object
stream	stream
reference	reference
mapping	mapping
args	ars
defaults	defaults

Details

The availableDefaultMappings function can be used to find out whether the package defines a mapping scheme between one of the many supported input file types and the metadata columns of the tracks' GRanges objects.

Value

Constructor functions of AnnotationTrack, DataTrack, SequenceTrack and ⁠AlignmentsTrack`` can create a special object of corresponding ⁠Reference*Track' subclass with pointer to the referenced file.

A virtual class: No objects may be created from it.

Functions

• availableDefaultMapping(): Function to find out whether the package defines a mapping scheme between one of the many supported input file types and the metadata columns of the tracks's GRanges objects.

• initialize(ReferenceTrack): Initialize.

Slots

stream

Object of class function. The import function to stream data of the file system. Needs to be able to handle the two mandatory arguments file (a character containing a valid file path) and selection (a GRanges object with the genomic region to plot).

reference

Object of class "character", the path to the file containing the data.

mapping

Object of class list, a default mapping between the metadata columns of the returned GRanges object from the import function and the elemenMetadata columns that make up the final track object.

args

Object of class list, the passed in constructor arguments during object instantiation. Those will be needed when fetching the data in order to fill all necessary slots.

defaults

Object of class list, the relevant default values to be used when neither mapping nor args provides the necessary information.

Author(s)

Florian Hahne

See Also

DisplayPars

GdObject

GRanges

HighlightTrack

ImageMap

IRanges

RangeTrack

DataTrack

collapsing

grouping

panel.grid

plotTracks

settings

Examples

# This is a reference class, below example from AlignmentsTrack

afrom <- 2960000
ato <- 3160000
alTrack <- AlignmentsTrack(system.file(
    package = "Gviz", "extdata",
    "gapped.bam"
), isPaired = TRUE)
plotTracks(alTrack, from = afrom, to = ato, chromosome = "chr12")

ivanek/Gviz documentation built on Nov. 20, 2023, 8:16 p.m.