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GenomeGraphs (version 1.32.0)

Plotting genomic information from Ensembl

Description

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system.

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Version

Version

1.32.0

License

Artistic-2.0

Maintainer

Steffen Durinck

Last Published

February 15th, 2017

Functions in GenomeGraphs (1.32.0)

Class "Overlay"

geneRegionBiomart

Construct an AnnotationTrack object from biomaRt.

Class "Gene" represents the Ensembl Gene level annotation

Generic called on each gdObject to do the plotting.

Class "gdObject" is the parent class of all of the objects in the system.

Retrieves a display parameter from an object.

Class "Legend", represents a legend to add to a plot

makeGenericArray

Creates an object of class GenericArray

Creates object of class Ideogram

gdPlot is the main plotting function of the GenomeGraphs package

makeSegmentation

Create objects of class segmentation

Creates an object of class BaseTrack

Contains dummy expression array probe start positions

Transcript-class

Represent known transcript isoforms as annoted by Ensembl

TrackOverlay-class

Class "TrackOverlay"

DisplayPars constructs objects of type DisplayPars which are used to effect the display of gdObjects

Creates an object of class Gene containing the intron-exon structures of genes

Creates an object of class Legend

This is an example data set from chromosome 4 of yeast from various publicly available datasets.

Sets a display parameter

GeneRegion-class

Class "GeneRegion", representing gene structures in a defined genomic region

GenericArray-class

Class "GenericArray", representing array data

Creates an object of class GeneModel

Contains dummy exon probe positions

Create objects of class Smoothing

Contains exon array data

GenomeAxis-class

Class "GenomeAxis", representing a genomic coordinate axis

GeneModel-class

Class "GeneModel", represents a custom gene model

showDisplayOptions

Print standard display options, DisplayPars for an object or a class

drawTrackOverlay-methods

This method does the drawing of a track overlay. One should implement this method to gain track plotting functionality.

Contains dummy copy number data

Contains dummy copy number segment data

Class "Ideogram", represent an Ideogram

TranscriptRegion-class

Class "TranscriptRegion", representing a genomic region with transcripts

Contains info to plot ideograms

Contains dummy copy number segmentation end positions

makeTextOverlay

Create objects of class TextOverlay

DisplayPars-class

Class "DisplayPars" is used to specify graphical parameters to gdObjects.

Segmentation-class

Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack)

Contains probe start and end positions of exon array probes

Smoothing-class

Class "Smoothing"

makeAnnotationTrack

Create objects of class AnnotationTrack

Contains exon array data

Contains dummy yeast conservation data

BaseTrack-class

Class "BaseTrack" represents base specific data

ExonArray-class

Class "ExonArray" representing probe level exon array data from Affymetrix

RectangleOverlay-class

Class "RectangleOverlay"

Creates and object of class ExonArray

Creates an object of class GenomeAxis

TextOverlay-class

Class "TextOverlay"

Creates an object of class Gene

Contains dummy intensity data

getGenomicRange

Retrieves the genomic range of an object

AnnotationTrack-class

Class "AnnotationTrack"

HighlightRegion-class

Class "HighlightRegion" is used to highlight vertical blocks of genomic regions.

MappedRead-class

Represents mapped reads

Class "Title" representing the title of a plot

ImplementsTrackOverlay-class

Class "ImplementsTrackOverlay"

AnnotationTrack objects from biomaRt

makeRectangleOverlay

Create a rectangular overlay

Creates an object of class Title

Creates an object of class Transcript

Contains dummy copy number segmentation start positions data