Gviz: Plotting data and annotation information along genomic coordinates

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC 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.

Author
Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou, Ge Tan <ge.tan09@imperial.ac.uk>, Lance Parsons <lparsons@princeton.edu>, Shraddha Pai <shraddha.pai@utoronto.ca>
Date of publication
None
Maintainer
Florian Hahne <florian.hahne@novartis.com>
License
Artistic-2.0
Version
1.18.1

View on Bioconductor

Man pages

AlignedReadTrack-class
AlignedReadTrack class and methods (NOTE: THIS IS STILL IN...
AlignmentsTrack-class
AlignmentsTrack class and methods
AnnotationTrack-class
AnnotationTrack class and methods
BiomartGeneRegionTrack-class
BiomartGeneRegionTrack class and methods
collapsing
Dynamic content based on the available resolution
CustomTrack-class
CustomTrack class and methods
datasets
Data sets
DataTrack-class
DataTrack class and methods
DisplayPars-class
DisplayPars class and method
exportTracks
Export GenomeGraph tracks to a annotation file...
GdObject-class
GdObject class and methods
GeneRegionTrack-class
GeneRegionTrack class and methods
GenomeAxisTrack-class
GenomeAxisTrack class and methods
grouping
Grouping of annotation features
HighlightTrack-class
HighlightTrack class and methods
IdeogramTrack-class
IdeogramTrack class and methods
ImageMap-class
ImageMap class and methods
NumericTrack-class
NumericTrack class and methods
OverlayTrack-class
OverlayTrack class and methods
plotTracks
The main plotting function for one or several GenomeGraph...
RangeTrack-class
RangeTrack class and methods
ReferenceTrack-class
ReferenceTrack class and methods
SequenceTrack-class
SequenceTrack class and methods
settings
Setting display parameters to control the look and feel of...
StackedTrack-class
StackedTrack class and methods
UcscTrack
Meta-constructor for GenomeGraph tracks fetched directly from...

Files in this package

Gviz/DESCRIPTION
Gviz/NAMESPACE
Gviz/NEWS
Gviz/R
Gviz/R/AllClasses.R
Gviz/R/AllGenerics.R
Gviz/R/Gviz-methods.R
Gviz/R/Gviz.R
Gviz/Rplots.pdf
Gviz/TODO
Gviz/build
Gviz/build/vignette.rds
Gviz/data
Gviz/data/alTrackGenes.rda
Gviz/data/biomTrack.rda
Gviz/data/bmTrack.rda
Gviz/data/collapseTrack.rda
Gviz/data/cpgIslands.rda
Gviz/data/cyp2b10.rda
Gviz/data/denseAnnTrack.rda
Gviz/data/dtHoriz.rda
Gviz/data/geneDetails.rda
Gviz/data/geneModels.rda
Gviz/data/idTrack.rda
Gviz/data/itrack.rda
Gviz/data/twoGroups.rda
Gviz/data/ucscItems.rda
Gviz/inst
Gviz/inst/CITATION
Gviz/inst/doc
Gviz/inst/doc/Gviz.R
Gviz/inst/doc/Gviz.Rnw
Gviz/inst/doc/Gviz.pdf
Gviz/inst/extdata
Gviz/inst/extdata/GSM461176_S2_DRSC_Untreated_1_bmm.bam
Gviz/inst/extdata/GSM461176_S2_DRSC_Untreated_1_bmm.bam.bai
Gviz/inst/extdata/GSM461179_S2_DRSC_CG8144_RNAi_1_bmm.bam
Gviz/inst/extdata/GSM461179_S2_DRSC_CG8144_RNAi_1_bmm.bam.bai
Gviz/inst/extdata/biomartVersionsLatest.txt
Gviz/inst/extdata/biomartVersionsNow.txt
Gviz/inst/extdata/gapped.bam
Gviz/inst/extdata/gapped.bam.bai
Gviz/inst/extdata/snps.bam
Gviz/inst/extdata/snps.bam.bai
Gviz/inst/extdata/test.2bit
Gviz/inst/extdata/test.bam
Gviz/inst/extdata/test.bam.bai
Gviz/inst/extdata/test.bed
Gviz/inst/extdata/test.bedGraph
Gviz/inst/extdata/test.bw
Gviz/inst/extdata/test.fa
Gviz/inst/extdata/test.fa.fai
Gviz/inst/extdata/test.gff
Gviz/inst/extdata/test.gff1
Gviz/inst/extdata/test.gff2
Gviz/inst/extdata/test.gff3
Gviz/inst/extdata/test.gtf
Gviz/inst/extdata/test.wig
Gviz/inst/lib
Gviz/inst/lib/testUCSC.pl
Gviz/inst/lib/ucscUrl.pl
Gviz/inst/scripts
Gviz/inst/scripts/documentation.R
Gviz/inst/scripts/functionality.R
Gviz/inst/scripts/loadIntoEnv.R
Gviz/inst/scripts/sourcePackage.R
Gviz/inst/scripts/testBiomartGenomeMappings.R
Gviz/inst/scripts/testing.R
Gviz/inst/scripts/updateBiomartGenomeMappings.R
Gviz/man
Gviz/man/AlignedReadTrack-class.Rd
Gviz/man/AlignmentsTrack-class.Rd
Gviz/man/AnnotationTrack-class.Rd
Gviz/man/BiomartGeneRegionTrack-class.Rd
Gviz/man/CustomTrack-class.Rd
Gviz/man/DataTrack-class.Rd
Gviz/man/DisplayPars-class.Rd
Gviz/man/GdObject-class.Rd
Gviz/man/GeneRegionTrack-class.Rd
Gviz/man/GenomeAxisTrack-class.Rd
Gviz/man/HighlightTrack-class.Rd
Gviz/man/IdeogramTrack-class.Rd
Gviz/man/ImageMap-class.Rd
Gviz/man/NumericTrack-class.Rd
Gviz/man/OverlayTrack-class.Rd
Gviz/man/RangeTrack-class.Rd
Gviz/man/ReferenceTrack-class.Rd
Gviz/man/SequenceTrack-class.Rd
Gviz/man/StackedTrack-class.Rd
Gviz/man/UcscTrack.Rd
Gviz/man/collapsing.Rd
Gviz/man/datasets.Rd
Gviz/man/exportTracks.Rd
Gviz/man/grouping.Rd
Gviz/man/plotTracks.Rd
Gviz/man/settings.Rd
Gviz/vignettes
Gviz/vignettes/Gviz-refs.bib
Gviz/vignettes/Gviz.Rnw
Gviz/vignettes/ucsc1.pdf
Gviz/vignettes/ucsc2.pdf