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.

AuthorSteffen Durinck <sdurinck@gmail.com>, James Bullard <bullard@berkeley.edu>
Date of publicationNone
MaintainerSteffen Durinck <sdurinck@gmail.com>
LicenseArtistic-2.0
Version1.34.0

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

Functions

AnnotationTrack-class Man page
BaseTrack-class Man page
cn Man page
DisplayPars Man page
DisplayPars-class Man page
drawGD Man page
drawGD,AnnotationTrack-method Man page
drawGD,BaseTrack-method Man page
drawGD,ExonArray-method Man page
drawGD,Gene-method Man page
drawGD,GeneModel-method Man page
drawGD,GeneRegion-method Man page
drawGD,GenericArray-method Man page
drawGD,GenomeAxis-method Man page
drawGD,Ideogram-method Man page
drawGD,Legend-method Man page
drawGD,MappedRead-method Man page
drawGD,Segmentation-method Man page
drawGD,Title-method Man page
drawGD,Transcript-method Man page
drawOverlay,RectangleOverlay-method Man page
drawOverlay, TextOverlay-method Man page
drawTrackOverlay-methods Man page
drawTrackOverlay,Segmentation-method Man page
drawTrackOverlay,Smoothing-method Man page
ExonArray-class Man page
exonProbePos Man page
gdObject-class Man page
gdPlot Man page
geneBiomart Man page
Gene-class Man page
GeneModel-class Man page
geneRegionBiomart Man page
GeneRegion-class Man page
GenericArray-class Man page
GenomeAxis-class Man page
getCex,gdObject-method Man page
getColor,gdObject-method Man page
getGenomicRange Man page
getGenomicRange,BaseTrack-method Man page
getGenomicRange,ExonArray-method Man page
getGenomicRange,gdObject-method Man page
getGenomicRange,Gene-method Man page
getGenomicRange,GeneRegion-method Man page
getGenomicRange,GenericArray-method Man page
getGenomicRange,Transcript-method Man page
getGenomicRange,TranscriptRegion-method Man page
getLty,gdObject-method Man page
getLwd,gdObject-method Man page
getPar Man page
getPar,DisplayPars-method Man page
getPar,gdObject-method Man page
getPch,gdObject-method Man page
getPlotId,AnnotationTrack-method Man page
getPointSize,gdObject-method Man page
getSegmentEnd,Segmentation-method Man page
getSegments,Segmentation-method Man page
getSegmentStart,Segmentation-method Man page
getSize Man page
getSize,gdObject-method Man page
HighlightRegion-class Man page
Ideogram-class Man page
ideogramTab Man page
ImplementsTrackOverlay-class Man page
initialize,AnnotationTrack-method Man page
initialize,DisplayPars-method Man page
initialize,gdObject-method Man page
initialize,Gene-method Man page
initialize,GeneRegion-method Man page
initialize,Transcript-method Man page
intensity Man page
Legend-class Man page
makeAnnotationTrack Man page
makeBaseTrack Man page
makeExonArray Man page
makeGene Man page
makeGeneModel Man page
makeGeneRegion Man page
makeGenericArray Man page
makeGenomeAxis Man page
makeIdeogram Man page
makeLegend Man page
makeRectangleOverlay Man page
makeSegmentation Man page
makeSmoothing Man page
makeTextOverlay Man page
makeTitle Man page
makeTranscript Man page
MappedRead-class Man page
Overlay-class Man page
probestart Man page
RectangleOverlay-class Man page
segEnd Man page
Segmentation-class Man page
segments Man page
segStart Man page
seqDataEx Man page
setPar Man page
setPar,DisplayPars-method Man page
setPar,gdObject-method Man page
show,BaseTrack-method Man page
showDisplayOptions Man page
showDisplayOptions,character-method Man page
showDisplayOptions,gdObject-method Man page
show,DisplayPars-method Man page
show,ExonArray-method Man page
show,Gene-method Man page
show,GeneRegion-method Man page
show,GenericArray-method Man page
show,MappedRead-method Man page
show,Transcript-method Man page
show,TranscriptRegion-method Man page
Smoothing-class Man page
TextOverlay-class Man page
Title-class Man page
TrackOverlay-class Man page
Transcript-class Man page
TranscriptRegion-class Man page
unrData Man page
unrNProbes Man page
unrPositions Man page
yeastCons1 Man page

Files

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

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