# Plotting genomic information from Ensembl

## Documentation for package ‘GenomeGraphs’ version 1.8.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

A B C D E G H I L M O P R S T U Y

## -- A --

AnnotationTrack-class | Class "AnnotationTrack"

## -- B --

BaseTrack-class | Class "BaseTrack" represents base specific data

## -- C --

cn | Contains dummy copy number data

## -- D --

DisplayPars | DisplayPars constructs objects of type DisplayPars which are used to effect the display of gdObjects
DisplayPars-class | Class "DisplayPars" is used to specify graphical parameters to gdObjects.
drawGD | Generic called on each gdObject to do the plotting.
drawGD-method | Class "AnnotationTrack"
drawGD-method | Class "BaseTrack" represents base specific data
drawGD-method | Class "ExonArray" representing probe level exon array data from Affymetrix
drawGD-method | Class "Gene" represents the Ensembl Gene level annotation
drawGD-method | Class "GeneModel", represents a custom gene model
drawGD-method | Class "GeneRegion", representing gene structures in a defined genomic region
drawGD-method | Class "GenericArray", representing array data
drawGD-method | Class "GenomeAxis", representing a genomic coordinate axis
drawGD-method | Class "Ideogram", represent an Ideogram
drawGD-method | Class "Legend", represents a legend to add to a plot
drawGD-method | Represents mapped reads
drawGD-method | Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack)
drawGD-method | Class "Title" representing the title of a plot
drawGD-method | Represent known transcript isoforms as annoted by Ensembl
drawOverlay-method | Class "RectangleOverlay"
drawOverlay-method | Class "TextOverlay"
drawTrackOverlay-method | This method does the drawing of a track overlay. One should implement this method to gain track plotting functionality.
drawTrackOverlay-methods | This method does the drawing of a track overlay. One should implement this method to gain track plotting functionality.

## -- E --

ExonArray-class | Class "ExonArray" representing probe level exon array data from Affymetrix
exonProbePos | Contains dummy exon probe positions

## -- G --

gdObject-class | Class "gdObject" is the parent class of all of the objects in the system.
gdPlot | gdPlot is the main plotting function of the GenomeGraphs package
Gene-class | Class "Gene" represents the Ensembl Gene level annotation
geneBiomart | AnnotationTrack objects from biomaRt
GeneModel-class | Class "GeneModel", represents a custom gene model
GeneRegion-class | Class "GeneRegion", representing gene structures in a defined genomic region
geneRegionBiomart | Construct an AnnotationTrack object from biomaRt.
GenericArray-class | Class "GenericArray", representing array data
GenomeAxis-class | Class "GenomeAxis", representing a genomic coordinate axis
getCex-method | Class "gdObject" is the parent class of all of the objects in the system.
getColor-method | Class "gdObject" is the parent class of all of the objects in the system.
getLty-method | Class "gdObject" is the parent class of all of the objects in the system.
getLwd-method | Class "gdObject" is the parent class of all of the objects in the system.
getPar | Retrieves a display parameter from an object.
getPar-method | Class "DisplayPars" is used to specify graphical parameters to gdObjects.
getPar-method | Class "gdObject" is the parent class of all of the objects in the system.
getPch-method | Class "gdObject" is the parent class of all of the objects in the system.
getPlotId-method | Class "AnnotationTrack"
getPointSize-method | Class "gdObject" is the parent class of all of the objects in the system.
getSegmentEnd-method | Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack)
getSegments-method | Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack)
getSegmentStart-method | Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack)
getSize-method | Class "gdObject" is the parent class of all of the objects in the system.

## -- H --

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

## -- I --

Ideogram-class | Class "Ideogram", represent an Ideogram
ideogramTab | Contains info to plot ideograms
ImplementsTrackOverlay-class | Class "ImplementsTrackOverlay"
initialize-method | Class "AnnotationTrack"
initialize-method | Class "DisplayPars" is used to specify graphical parameters to gdObjects.
initialize-method | Class "Gene" represents the Ensembl Gene level annotation
initialize-method | Class "GeneRegion", representing gene structures in a defined genomic region
initialize-method | Represent known transcript isoforms as annoted by Ensembl
initialize-method | Class "gdObject" is the parent class of all of the objects in the system.
intensity | Contains dummy intensity data

## -- L --

Legend-class | Class "Legend", represents a legend to add to a plot

## -- M --

makeAnnotationTrack | Create objects of class AnnotationTrack
makeBaseTrack | Creates an object of class BaseTrack
makeExonArray | Creates and object of class ExonArray
makeGene | Creates an object of class Gene
makeGeneModel | Creates an object of class GeneModel
makeGeneRegion | Creates an object of class Gene containing the intron-exon structures of genes
makeGenericArray | Creates an object of class GenericArray
makeGenomeAxis | Creates an object of class GenomeAxis
makeIdeogram | Creates object of class Ideogram
makeLegend | Creates an object of class Legend
makeRectangleOverlay | Create a rectangular overlay
makeSegmentation | Create objects of class segmentation
makeSmoothing | Create objects of class Smoothing
makeTextOverlay | Create objects of class TextOverlay
makeTitle | Creates an object of class Title
makeTranscript | Creates an object of class Transcript
MappedRead-class | Represents mapped reads

## -- O --

Overlay-class | Class "Overlay"

## -- P --

probestart | Contains dummy expression array probe start positions

## -- R --

RectangleOverlay-class | Class "RectangleOverlay"

## -- S --

segEnd | Contains dummy copy number segmentation end positions
Segmentation-class | Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack)
segments | Contains dummy copy number segment data
segStart | Contains dummy copy number segmentation start positions data
seqDataEx | This is an example data set from chromosome 4 of yeast from various publicly available datasets.
setPar | Sets a display parameter
setPar-method | Class "DisplayPars" is used to specify graphical parameters to gdObjects.
setPar-method | Class "gdObject" is the parent class of all of the objects in the system.
show-method | Class "BaseTrack" represents base specific data
show-method | Class "DisplayPars" is used to specify graphical parameters to gdObjects.
show-method | Class "ExonArray" representing probe level exon array data from Affymetrix
show-method | Class "Gene" represents the Ensembl Gene level annotation
show-method | Class "GeneRegion", representing gene structures in a defined genomic region
show-method | Class "GenericArray", representing array data
show-method | Represents mapped reads
show-method | Represent known transcript isoforms as annoted by Ensembl
show-method | Class "TranscriptRegion", representing a genomic region with transcripts
showDisplayOptions | Print standard display options, DisplayPars for an object or a class
showDisplayOptions-method | Class "gdObject" is the parent class of all of the objects in the system.
Smoothing-class | Class "Smoothing"

## -- T --

TextOverlay-class | Class "TextOverlay"
Title-class | Class "Title" representing the title of a plot
TrackOverlay-class | Class "TrackOverlay"
Transcript-class | Represent known transcript isoforms as annoted by Ensembl
TranscriptRegion-class | Class "TranscriptRegion", representing a genomic region with transcripts

## -- U --

unrData | Contains exon array data
unrNProbes | Contains exon array data
unrPositions | Contains probe start and end positions of exon array probes

## -- Y --

yeastCons1 | Contains dummy yeast conservation data