# Plotting data and annotation information along genomic coordinates

## Documentation for package ‘Gviz’ version 1.40.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I K L M N P R S T U V W misc

## -- A --

addScheme | Setting display parameters to control the look and feel of the plots
AlignmentsTrack | AlignmentsTrack class and methods
AlignmentsTrack-class | AlignmentsTrack class and methods
as.list-method | DisplayPars: A class to control the plotting parameters for GdObjects
availableDefaultMapping | ReferenceTrack class and methods
availableDisplayPars | DisplayPars: A class to control the plotting parameters for GdObjects
axTrack | Data sets

## -- B --

BiomartGeneRegionTrack | BiomartGeneRegionTrack class and methods
BiomartGeneRegionTrack-class | BiomartGeneRegionTrack class and methods
biomTrack | Data sets
biomTrack2 | Data sets
bmt | Data sets
bmTrack | Data sets

## -- C --

chromosome-method | RangeTrack class and methods
chromosome-method | SequenceTrack class and methods
chromosome<--method | AlignmentsTrack class and methods
chromosome<--method | HighlightTrack class and methods
chromosome<--method | IdeogramTrack class and methods
chromosome<--method | RangeTrack class and methods
chromosome<--method | SequenceTrack class and methods
clearSessionCache | Meta-constructor for Gviz tracks fetched directly from the various UCSC data sources.
collapsing | Dynamic content based on the available resolution
conservation | Data sets
consolidateTrack-method | HighlightTrack class and methods
consolidateTrack-method | RangeTrack class and methods
consolidateTrack-method | SequenceTrack class and methods
consolidateTrack-method | StackedTrack class and methods
cpgIslands | Data sets
ctrack | Data sets
CustomTrack | CustomTrack class and methods
CustomTrack-class | CustomTrack class and methods
cyp2b10 | Data sets

## -- D --

datasets | Data sets
denseAnnTrack | Data sets
DisplayPars | DisplayPars: A class to control the plotting parameters for GdObjects
displayPars | DisplayPars: A class to control the plotting parameters for GdObjects
DisplayPars-class | DisplayPars: A class to control the plotting parameters for GdObjects
displayPars-method | DisplayPars: A class to control the plotting parameters for GdObjects
displayPars<- | DisplayPars: A class to control the plotting parameters for GdObjects
displayPars<--method | DisplayPars: A class to control the plotting parameters for GdObjects
displayPars<--method | HighlightTrack class and methods
drawAxis-method | AlignmentsTrack class and methods
drawAxis-method | NumericTrack class and methods
drawGD-method | AlignmentsTrack class and methods
drawGD-method | CustomTrack class and methods
drawGD-method | GeneRegionTrack class and methods
drawGD-method | IdeogramTrack class and methods
drawGD-method | SequenceTrack class and methods
drawGD-method | StackedTrack class and methods
drawGrid-method | NumericTrack class and methods
dtHoriz | Data sets

## -- E --

end-method | IdeogramTrack class and methods
end-method | RangeTrack class and methods
end-method | SequenceTrack class and methods
end<--method | IdeogramTrack class and methods
end<--method | RangeTrack class and methods
ensGenes | Data sets
exon-method | GeneRegionTrack class and methods
exon<--method | GeneRegionTrack class and methods
exportTracks | Export Gviz tracks into an annotation file representation.

## -- F --

feature-method | RangeTrack class and methods
feature<--method | RangeTrack class and methods
from | Data sets

## -- G --

gcContent | Data sets
gene-method | GeneRegionTrack class and methods
gene<--method | GeneRegionTrack class and methods
geneDetails | Data sets
geneModels | Data sets
GeneRegionTrack | GeneRegionTrack class and methods
GeneRegionTrack-class | GeneRegionTrack class and methods
genome-method | RangeTrack class and methods
genome-method | SequenceTrack class and methods
genome<--method | IdeogramTrack class and methods
genome<--method | RangeTrack class and methods
getPar | DisplayPars: A class to control the plotting parameters for GdObjects
getPar-method | DisplayPars: A class to control the plotting parameters for GdObjects
getScheme | Setting display parameters to control the look and feel of the plots
group-method | GeneRegionTrack class and methods
group<--method | GeneRegionTrack class and methods
grouping | Grouping of annotation features
Gviz-defunct | Defunct functions in package 'Gviz'
Gviz-deprecated | Deprecated functions in package 'Gviz'

## -- H --

HighlightTrack | HighlightTrack class and methods
HighlightTrack-class | HighlightTrack class and methods

## -- I --

identifier-method | GeneRegionTrack class and methods
identifier<--method | GeneRegionTrack class and methods
IdeogramTrack | IdeogramTrack class and methods
IdeogramTrack-class | IdeogramTrack class and methods
ideoTrack | Data sets
idTrack | Data sets
idxTrack | Data sets
initialize-method | AlignmentsTrack class and methods
initialize-method | BiomartGeneRegionTrack class and methods
initialize-method | CustomTrack class and methods
initialize-method | GeneRegionTrack class and methods
initialize-method | HighlightTrack class and methods
initialize-method | IdeogramTrack class and methods
initialize-method | RangeTrack class and methods
initialize-method | ReferenceTrack class and methods
initialize-method | SequenceTrack class and methods
initialize-method | StackedTrack class and methods
iTrack | Data sets
itrack | Data sets

## -- K --

knownGenes | Data sets

## -- L --

length-method | HighlightTrack class and methods
length-method | IdeogramTrack class and methods
length-method | RangeTrack class and methods
length-method | SequenceTrack class and methods

## -- M --

max-method | RangeTrack class and methods
min-method | RangeTrack class and methods

## -- N --

NumericTrack-class | NumericTrack class and methods

## -- P --

plotTracks | The main plotting function for one or several Gviz tracks.
position-method | IdeogramTrack class and methods
position-method | RangeTrack class and methods

## -- R --

range-method | RangeTrack class and methods
ranges-method | RangeTrack class and methods
RangeTrack-class | RangeTrack class and methods
ReferenceAlignmentsTrack-class | AlignmentsTrack class and methods
ReferenceGeneRegionTrack-class | GeneRegionTrack class and methods
ReferenceSequenceTrack-class | SequenceTrack class and methods
ReferenceTrack-class | ReferenceTrack class and methods
refGenes | Data sets
RNASequenceTrack | SequenceTrack class and methods

## -- S --

seqinfo-method | RangeTrack class and methods
seqlevels-method | RangeTrack class and methods
seqlevels-method | SequenceTrack class and methods
seqnames-method | RangeTrack class and methods
seqnames-method | SequenceTrack class and methods
SequenceBSgenomeTrack-class | SequenceTrack class and methods
SequenceDNAStringSetTrack-class | SequenceTrack class and methods
SequenceRNAStringSetTrack-class | SequenceTrack class and methods
SequenceTrack | SequenceTrack class and methods
SequenceTrack-class | SequenceTrack class and methods
setPar | DisplayPars: A class to control the plotting parameters for GdObjects
setPar-method | DisplayPars: A class to control the plotting parameters for GdObjects
setStacks-method | AlignmentsTrack class and methods
setStacks-method | HighlightTrack class and methods
setStacks-method | StackedTrack class and methods
settings | Setting display parameters to control the look and feel of the plots
show-method | AlignmentsTrack class and methods
show-method | CustomTrack class and methods
show-method | DisplayPars: A class to control the plotting parameters for GdObjects
show-method | GeneRegionTrack class and methods
show-method | HighlightTrack class and methods
show-method | IdeogramTrack class and methods
show-method | SequenceTrack class and methods
snpLocations | Data sets
split-method | RangeTrack class and methods
StackedTrack-class | StackedTrack class and methods
stacking-method | StackedTrack class and methods
stacking<--method | StackedTrack class and methods
stacks-method | AlignmentsTrack class and methods
stacks-method | StackedTrack class and methods
start-method | IdeogramTrack class and methods
start-method | RangeTrack class and methods
start-method | SequenceTrack class and methods
start<--method | IdeogramTrack class and methods
start<--method | RangeTrack class and methods
strand-method | RangeTrack class and methods
strand<--method | RangeTrack class and methods
subset-method | AlignmentsTrack class and methods
subset-method | BiomartGeneRegionTrack class and methods
subset-method | GeneRegionTrack class and methods
subset-method | HighlightTrack class and methods
subset-method | IdeogramTrack class and methods
subset-method | RangeTrack class and methods
subset-method | StackedTrack class and methods
symbol-method | GeneRegionTrack class and methods
symbol<--method | GeneRegionTrack class and methods

## -- T --

to | Data sets
transcript-method | GeneRegionTrack class and methods
transcript<--method | GeneRegionTrack class and methods
twoGroups | Data sets

## -- U --

UcscTrack | Meta-constructor for Gviz tracks fetched directly from the various UCSC data sources.

## -- V --

values-method | AlignmentsTrack class and methods
values-method | RangeTrack class and methods

## -- W --

width-method | IdeogramTrack class and methods
width-method | RangeTrack class and methods
width-method | SequenceTrack class and methods
width<--method | IdeogramTrack class and methods
width<--method | RangeTrack class and methods

## -- misc --

.DisplayPars | DisplayPars: A class to control the plotting parameters for GdObjects
[-method | IdeogramTrack class and methods
[-method | RangeTrack class and methods
[-method | StackedTrack class and methods