GenomeGraphs: Plotting genomic information from Ensembl

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.

Author
Steffen Durinck <sdurinck@gmail.com>, James Bullard <bullard@berkeley.edu>
Date of publication
None
Maintainer
Steffen Durinck <sdurinck@gmail.com>
License
Artistic-2.0
Version
1.34.0

View on Bioconductor

Man pages

AnnotationTrack-class
Class "AnnotationTrack"
BaseTrack-class
Class "BaseTrack" represents base specific data
cn
Contains dummy copy number data
DisplayPars
DisplayPars constructs objects of type DisplayPars which are...
DisplayPars-class
Class "DisplayPars" is used to specify graphical parameters...
drawGD
Generic called on each gdObject to do the plotting.
drawTrackOverlay-methods
This method does the drawing of a track overlay. One should...
ExonArray-class
Class "ExonArray" representing probe level exon array data...
exonProbePos
Contains dummy exon probe positions
gdObject-class
Class "gdObject" is the parent class of all of the objects in...
gdPlot
gdPlot is the main plotting function of the GenomeGraphs...
geneBiomart
AnnotationTrack objects from biomaRt
Gene-class
Class "Gene" represents the Ensembl Gene level annotation
GeneModel-class
Class "GeneModel", represents a custom gene model
geneRegionBiomart
Construct an AnnotationTrack object from biomaRt.
GeneRegion-class
Class "GeneRegion", representing gene structures in a defined...
GenericArray-class
Class "GenericArray", representing array data
GenomeAxis-class
Class "GenomeAxis", representing a genomic coordinate axis
getGenomicRange
Retrieves the genomic range of an object
getPar
Retrieves a display parameter from an object.
getSize
gets the size
HighlightRegion-class
Class "HighlightRegion" is used to highlight vertical blocks...
Ideogram-class
Class "Ideogram", represent an Ideogram
ideogramTab
Contains info to plot ideograms
ImplementsTrackOverlay-class
Class "ImplementsTrackOverlay"
intensity
Contains dummy intensity data
Legend-class
Class "Legend", represents a legend to add to a plot
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...
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
Overlay-class
Class "Overlay"
probestart
Contains dummy expression array probe start positions
RectangleOverlay-class
Class "RectangleOverlay"
segEnd
Contains dummy copy number segmentation end positions
Segmentation-class
Class "Segmentation" is used to specify segmentations to any...
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...
setPar
Sets a display parameter
showDisplayOptions
Print standard display options, DisplayPars for an object or...
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...
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

Files in this package

GenomeGraphs/DESCRIPTION
GenomeGraphs/NAMESPACE
GenomeGraphs/NEWS
GenomeGraphs/R
GenomeGraphs/R/GenomeGraphs-classes.R
GenomeGraphs/R/GenomeGraphs-methods.R
GenomeGraphs/R/GenomeGraphs.R
GenomeGraphs/R/Overlay.R
GenomeGraphs/build
GenomeGraphs/build/vignette.rds
GenomeGraphs/data
GenomeGraphs/data/exampleData.rda
GenomeGraphs/data/ideogram.rda
GenomeGraphs/data/seqDataEx.rda
GenomeGraphs/data/unrData.rda
GenomeGraphs/inst
GenomeGraphs/inst/doc
GenomeGraphs/inst/doc/GenomeGraphs.R
GenomeGraphs/inst/doc/GenomeGraphs.Rnw
GenomeGraphs/inst/doc/GenomeGraphs.pdf
GenomeGraphs/inst/extra
GenomeGraphs/inst/extra/dummyData.R
GenomeGraphs/man
GenomeGraphs/man/AnnotationTrack-class.Rd
GenomeGraphs/man/BaseTrack-class.Rd
GenomeGraphs/man/DisplayPars-class.Rd
GenomeGraphs/man/DisplayPars.Rd
GenomeGraphs/man/ExonArray-class.Rd
GenomeGraphs/man/Gene-class.Rd
GenomeGraphs/man/GeneModel-class.Rd
GenomeGraphs/man/GeneRegion-class.Rd
GenomeGraphs/man/GenericArray-class.Rd
GenomeGraphs/man/GenomeAxis-class.Rd
GenomeGraphs/man/HighlightRegion-class.Rd
GenomeGraphs/man/Ideogram-class.Rd
GenomeGraphs/man/ImplementsTrackOverlay-class.Rd
GenomeGraphs/man/Legend-class.Rd
GenomeGraphs/man/MappedRead-class.Rd
GenomeGraphs/man/Overlay-class.Rd
GenomeGraphs/man/RectangleOverlay-class.Rd
GenomeGraphs/man/Segmentation-class.Rd
GenomeGraphs/man/Smoothing-class.Rd
GenomeGraphs/man/TextOverlay-class.Rd
GenomeGraphs/man/Title-class.Rd
GenomeGraphs/man/TrackOverlay-class.Rd
GenomeGraphs/man/Transcript-class.Rd
GenomeGraphs/man/TranscriptRegion-class.Rd
GenomeGraphs/man/cn.Rd
GenomeGraphs/man/drawGD.Rd
GenomeGraphs/man/drawTrackOverlay-methods.Rd
GenomeGraphs/man/exonProbePos.Rd
GenomeGraphs/man/gdObject-class.Rd
GenomeGraphs/man/gdPlot.Rd
GenomeGraphs/man/geneBiomart.Rd
GenomeGraphs/man/geneRegionBiomart.Rd
GenomeGraphs/man/getGenomicRange.Rd
GenomeGraphs/man/getPar.Rd
GenomeGraphs/man/getSize.Rd
GenomeGraphs/man/ideogramTab.Rd
GenomeGraphs/man/intensity.Rd
GenomeGraphs/man/makeAnnotationTrack.Rd
GenomeGraphs/man/makeBaseTrack.Rd
GenomeGraphs/man/makeExonArray.Rd
GenomeGraphs/man/makeGene.Rd
GenomeGraphs/man/makeGeneModel.Rd
GenomeGraphs/man/makeGeneRegion.Rd
GenomeGraphs/man/makeGenericArray.Rd
GenomeGraphs/man/makeGenomeAxis.Rd
GenomeGraphs/man/makeIdeogram.Rd
GenomeGraphs/man/makeLegend.Rd
GenomeGraphs/man/makeRectangleOverlay.Rd
GenomeGraphs/man/makeSegmentation.Rd
GenomeGraphs/man/makeSmoothing.Rd
GenomeGraphs/man/makeTextOverlay.Rd
GenomeGraphs/man/makeTitle.Rd
GenomeGraphs/man/makeTranscript.Rd
GenomeGraphs/man/probestart.Rd
GenomeGraphs/man/segEnd.Rd
GenomeGraphs/man/segStart.Rd
GenomeGraphs/man/segments.Rd
GenomeGraphs/man/seqDataEx.Rd
GenomeGraphs/man/setPar.Rd
GenomeGraphs/man/showDisplayOptions.Rd
GenomeGraphs/man/unrData.Rd
GenomeGraphs/man/unrNProbes.Rd
GenomeGraphs/man/unrPositions.Rd
GenomeGraphs/man/yeastCons1.Rd
GenomeGraphs/vignettes
GenomeGraphs/vignettes/GenomeGraphs.Rnw