AnnotationTrack-class Class "AnnotationTrack" BaseTrack-class Class "BaseTrack" represents base specific data 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. ExonArray-class Class "ExonArray" representing probe level exon array data from Affymetrix Gene-class Class "Gene" represents the Ensembl Gene level annotation GeneModel-class Class "GeneModel", represents a custom gene model GeneRegion-class Class "GeneRegion", representing gene structures in a defined genomic region GenericArray-class Class "GenericArray", representing array data GenomeAxis-class Class "GenomeAxis", representing a genomic coordinate axis HighlightRegion-class Class "HighlightRegion" is used to highlight vertical blocks of genomic regions. Ideogram-class Class "Ideogram", represent an Ideogram ImplementsTrackOverlay-class Class "ImplementsTrackOverlay" Legend-class Class "Legend", represents a legend to add to a plot MappedRead-class Represents mapped reads Overlay-class Class "Overlay" RectangleOverlay-class Class "RectangleOverlay" Segmentation-class Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack) Smoothing-class Class "Smoothing" 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 cn Contains dummy copy number data drawGD Generic called on each gdObject to do the plotting. drawTrackOverlay-methods This method does the drawing of a track overlay. One should implement this method to gain track plotting functionality. exonProbePos Contains dummy exon probe positions 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 geneBiomart AnnotationTrack objects from biomaRt geneRegionBiomart Construct an AnnotationTrack object from biomaRt. getGenomicRange Retrieves the genomic range of an object getPar Retrieves a display parameter from an object. getSize gets the size ideogramTab Contains info to plot ideograms intensity Contains dummy intensity data 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 probestart Contains dummy expression array probe start positions segEnd Contains dummy copy number segmentation end positions segStart Contains dummy copy number segmentation start positions data segments Contains dummy copy number segment data seqDataEx This is an example data set from chromosome 4 of yeast from various publicly available datasets. setPar Sets a display parameter showDisplayOptions Print standard display options, DisplayPars for an object or a class unrData Contains exon array data unrNProbes Contains exon array data unrPositions Contains probe start and end positions of exon array probes yeastCons1 Contains dummy yeast conservation data