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Gviz (version 1.16.1)

Plotting data and annotation information along genomic coordinates

Description

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.

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Version

Version

1.16.1

License

Artistic-2.0

Maintainer

Florian Hahne

Last Published

February 15th, 2017

Functions in Gviz (1.16.1)

settings

Setting display parameters to control the look and feel of the plots
exportTracks

Export GenomeGraph tracks to a annotation file representation.
collapsing

Dynamic content based on the available resolution
grouping

Grouping of annotation features
RangeTrack-class

RangeTrack class and methods
BiomartGeneRegionTrack-class

BiomartGeneRegionTrack class and methods
SequenceTrack-class

SequenceTrack class and methods
AlignedReadTrack-class

AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE)
GenomeAxisTrack-class

GenomeAxisTrack class and methods
IdeogramTrack-class

IdeogramTrack class and methods
ReferenceTrack-class

ReferenceTrack class and methods
AlignmentsTrack-class

AlignmentsTrack class and methods
DisplayPars-class

DisplayPars class and method
UcscTrack

Meta-constructor for GenomeGraph tracks fetched directly from the various UCSC data sources.
NumericTrack-class

NumericTrack class and methods
GeneRegionTrack-class

GeneRegionTrack class and methods
OverlayTrack-class

OverlayTrack class and methods
ImageMap-class

ImageMap class and methods
StackedTrack-class

StackedTrack class and methods
CustomTrack-class

CustomTrack class and methods
GdObject-class

GdObject class and methods
plotTracks

The main plotting function for one or several GenomeGraph tracks.
HighlightTrack-class

HighlightTrack class and methods
DataTrack-class

DataTrack class and methods
bmTrack

Data sets
AnnotationTrack-class

AnnotationTrack class and methods