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Table 1 Overview of classes representing drawable genomic datasets

From: GenomeGraphs: integrated genomic data visualization with R

Class

Description

gdObject

the root class of the system, never directly instantiated

DisplayPars

class managing various plotting parameters

Gene

class representing a gene

GeneRegion

class defining a region of a chromosome, generally a set of genetic elements (genes)

Transcript

class defining a transcript

TranscriptRegion

class defining a region of a chromosome, generally a set of genetic elements (transcripts)

Ideogram

class representing an ideogram

Title

class to draw a title

Legend

class to draw a legend

GenomeAxis

class to draw an axis

AnnotationTrack

class used to represent custom annotation

Overlay

root class for overlays, never directly instantiated

RectangleOverlay

class to represent rectangular regions of interest

TextOverlay

class to draw text on plots

Segmentation

class to draw horizontal lines in various sets of data

GenericArray

class to draw data from microarrays.

ExonArray

class to draw data from exon microarrays.

GeneModel

class to draw custom gene models (intron-exon structures)

BaseTrack

class to draw arbitrary data at a given base

MappedRead

class to plot sequencing reads that are mapped to the genome

  1. The main class, of which all other drawable classes are subclasses of, is the gdObject class. The Gene, Transcript, and GeneRegion classes are subclasses of gdObject and represent annotation data that are retrieved on-line from Ensembl upon creation of these objects. The third set of classes represent experimental data such as microarray and copy number data which can both be modeled using the GenericArray class. Probe-level exon array data can be represented by the ExonArray class and base-specific values such as nucleotide conservation scores among different species are represented by the BaseTrack class.