# Plotting data and annotation information along genomic coordinates

## Documentation for package ‘Gviz’ version 1.8.4

- 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 O P R S T U V W misc

## -- A --

addScheme | Setting display parameters to control the look and feel of the plots
AlignedReadTrack | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE)
AlignedReadTrack-class | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE)
AlignmentsTrack | AlignmentsTrack class and methods
AlignmentsTrack-class | AlignmentsTrack class and methods
AnnotationTrack | AnnotationTrack class and methods
AnnotationTrack-class | AnnotationTrack class and methods
as.list-method | DisplayPars class and method
availableDefaultMapping | ReferenceTrack class and methods
availableDisplayPars | DisplayPars class and method
axTrack | Data sets

## -- B --

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

## -- C --

chromosome | RangeTrack class and methods
chromosome-method | GdObject class and methods
chromosome-method | RangeTrack class and methods
chromosome-method | SequenceTrack class and methods
chromosome<- | RangeTrack class and methods
chromosome<--method | AlignmentsTrack class and methods
chromosome<--method | GdObject 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 GenomeGraph tracks fetched directly from the various UCSC data sources.
coerce-method | AnnotationTrack class and methods
coerce-method | DataTrack class and methods
coerce-method | DisplayPars class and method
coerce-method | GeneRegionTrack class and methods
coerce-method | RangeTrack class and methods
coerce-method | SequenceTrack class and methods
collapseTrack-method | AnnotationTrack class and methods
collapseTrack-method | DataTrack class and methods
collapseTrack-method | GeneRegionTrack class and methods
collapseTrack-method | GenomeAxisTrack class and methods
collapsing | Dynamic content based on the available resolution
conservation | Data sets
consolidateTrack | GdObject class and methods
consolidateTrack-method | AnnotationTrack class and methods
consolidateTrack-method | GdObject class and methods
consolidateTrack-method | HighlightTrack class and methods
consolidateTrack-method | OverlayTrack class and methods
consolidateTrack-method | RangeTrack class and methods
consolidateTrack-method | SequenceTrack class and methods
consolidateTrack-method | StackedTrack class and methods
coords | GdObject class and methods
coords-method | GdObject class and methods
coords-method | ImageMap class and methods
coverage-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE)
coverage-method | AlignmentsTrack class and methods
cpgIslands | Data sets
ctrack | Data sets
cyp2b10 | Data sets

## -- D --

DataTrack | DataTrack class and methods
DataTrack-class | DataTrack class and methods
denseAnnTrack | Data sets
DetailsAnnotationTrack | AnnotationTrack class and methods
DetailsAnnotationTrack-class | AnnotationTrack class and methods
DisplayPars | DisplayPars class and method
displayPars | DisplayPars class and method
DisplayPars-class | DisplayPars class and method
displayPars-method | DisplayPars class and method
displayPars-method | GdObject class and methods
displayPars<- | DisplayPars class and method
displayPars<--method | DisplayPars class and method
displayPars<--method | GdObject class and methods
drawAxis-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE)
drawAxis-method | AlignmentsTrack class and methods
drawAxis-method | DataTrack class and methods
drawAxis-method | GdObject class and methods
drawAxis-method | NumericTrack class and methods
drawGD | GdObject class and methods
drawGD-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE)
drawGD-method | AlignmentsTrack class and methods
drawGD-method | AnnotationTrack class and methods
drawGD-method | DataTrack class and methods
drawGD-method | GdObject class and methods
drawGD-method | GenomeAxisTrack class and methods
drawGD-method | IdeogramTrack class and methods
drawGD-method | OverlayTrack class and methods
drawGD-method | StackedTrack class and methods
drawGrid-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE)
drawGrid-method | AnnotationTrack class and methods
drawGrid-method | GdObject class and methods
drawGrid-method | NumericTrack class and methods
dtHoriz | Data sets

## -- E --

end-method | GenomeAxisTrack class and methods
end-method | IdeogramTrack class and methods
end-method | RangeTrack class and methods
end-method | SequenceTrack class and methods
end<--method | GenomeAxisTrack class and methods
end<--method | IdeogramTrack class and methods
end<--method | RangeTrack class and methods
ensGenes | Data sets
exon | GeneRegionTrack class and methods
exon-method | GeneRegionTrack class and methods
exon<- | GeneRegionTrack class and methods
exon<--method | GeneRegionTrack class and methods
exportTracks | Export GenomeGraph tracks to a annotation file representation.

## -- F --

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

## -- G --

gcContent | Data sets
GdObject | GdObject class and methods
GdObject-class | GdObject class and methods
gene | GeneRegionTrack class and methods
gene-method | GeneRegionTrack class and methods
gene<- | 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 | GdObject class and methods
genome<--method | IdeogramTrack class and methods
genome<--method | RangeTrack class and methods
GenomeAxisTrack | GenomeAxisTrack class and methods
GenomeAxisTrack-class | GenomeAxisTrack class and methods
getPar | DisplayPars class and method
getPar-method | DisplayPars class and method
getPar-method | GdObject class and methods
getScheme | Setting display parameters to control the look and feel of the plots
group | AnnotationTrack class and methods
group-method | AnnotationTrack class and methods
group-method | GdObject class and methods
group-method | GeneRegionTrack class and methods
group<- | AnnotationTrack class and methods
group<--method | AnnotationTrack class and methods
group<--method | GeneRegionTrack class and methods
grouping | Grouping of annotation features

## -- H --

head-method | DisplayPars class and method
HighlightTrack | HighlightTrack class and methods
HighlightTrack-class | HighlightTrack class and methods

## -- I --

identifier | AnnotationTrack class and methods
identifier-method | AnnotationTrack class and methods
identifier-method | GeneRegionTrack class and methods
identifier<- | AnnotationTrack class and methods
identifier<--method | AnnotationTrack 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
imageMap | GdObject class and methods
ImageMap-class | ImageMap class and methods
imageMap-method | GdObject class and methods
initialize-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE)
initialize-method | AlignmentsTrack class and methods
initialize-method | AnnotationTrack class and methods
initialize-method | BiomartGeneRegionTrack class and methods
initialize-method | DataTrack class and methods
initialize-method | DisplayPars class and method
initialize-method | GdObject class and methods
initialize-method | GeneRegionTrack class and methods
initialize-method | GenomeAxisTrack class and methods
initialize-method | HighlightTrack class and methods
initialize-method | IdeogramTrack class and methods
initialize-method | OverlayTrack 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
isActiveSeq-method | RangeTrack class and methods
isActiveSeq<--method | GdObject class and methods
itrack | Data sets

## -- K --

knownGenes | Data sets

## -- L --

length-method | GenomeAxisTrack class and methods
length-method | HighlightTrack class and methods
length-method | IdeogramTrack class and methods
length-method | OverlayTrack 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 --

names-method | GdObject class and methods
names<--method | GdObject class and methods
NumericTrack | NumericTrack class and methods
NumericTrack-class | NumericTrack class and methods

## -- O --

OverlayTrack | OverlayTrack class and methods
OverlayTrack-class | OverlayTrack class and methods

## -- P --

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

## -- R --

range | RangeTrack class and methods
range-method | DataTrack class and methods
range-method | GenomeAxisTrack class and methods
range-method | RangeTrack class and methods
ranges-method | GenomeAxisTrack class and methods
ranges-method | RangeTrack class and methods
ranges<--method | GenomeAxisTrack class and methods
ranges<--method | RangeTrack class and methods
RangeTrack | RangeTrack class and methods
RangeTrack-class | RangeTrack class and methods
ReferenceTrack | ReferenceTrack class and methods
ReferenceTrack-class | ReferenceTrack class and methods
refGenes | Data sets

## -- S --

score-method | DataTrack class and methods
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
SequenceTrack | SequenceTrack class and methods
SequenceTrack-class | SequenceTrack class and methods
setCoverage-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE)
setPar | DisplayPars class and method
setPar-method | DisplayPars class and method
setPar-method | GdObject class and methods
setStacks-method | AnnotationTrack class and methods
setStacks-method | HighlightTrack class and methods
setStacks-method | OverlayTrack class and methods
setStacks-method | StackedTrack class and methods
settings | Setting display parameters to control the look and feel of the plots
show-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE)
show-method | AlignmentsTrack class and methods
show-method | AnnotationTrack class and methods
show-method | DataTrack class and methods
show-method | DisplayPars class and method
show-method | GeneRegionTrack class and methods
show-method | GenomeAxisTrack class and methods
show-method | HighlightTrack class and methods
show-method | IdeogramTrack class and methods
show-method | OverlayTrack class and methods
snpLocations | Data sets
split-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE)
split-method | DataTrack class and methods
split-method | RangeTrack class and methods
StackedTrack | StackedTrack class and methods
StackedTrack-class | StackedTrack class and methods
stacking | StackedTrack class and methods
stacking-method | StackedTrack class and methods
stacking<- | StackedTrack class and methods
stacking<--method | StackedTrack class and methods
stacks | StackedTrack class and methods
stacks-method | AlignmentsTrack class and methods
stacks-method | StackedTrack class and methods
start-method | GenomeAxisTrack class and methods
start-method | IdeogramTrack class and methods
start-method | RangeTrack class and methods
start-method | SequenceTrack class and methods
start<--method | GenomeAxisTrack class and methods
start<--method | IdeogramTrack class and methods
start<--method | RangeTrack class and methods
strand-method | DataTrack class and methods
strand-method | GenomeAxisTrack class and methods
strand-method | RangeTrack class and methods
strand<--method | DataTrack class and methods
strand<--method | RangeTrack class and methods
subseq-method | SequenceTrack class and methods
subset-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE)
subset-method | AlignmentsTrack class and methods
subset-method | AnnotationTrack class and methods
subset-method | DataTrack class and methods
subset-method | GdObject class and methods
subset-method | GeneRegionTrack class and methods
subset-method | GenomeAxisTrack class and methods
subset-method | HighlightTrack class and methods
subset-method | IdeogramTrack class and methods
subset-method | OverlayTrack class and methods
subset-method | RangeTrack class and methods
subset-method | StackedTrack class and methods
symbol | GeneRegionTrack class and methods
symbol-method | GeneRegionTrack class and methods
symbol<- | GeneRegionTrack class and methods
symbol<--method | GeneRegionTrack class and methods

## -- T --

tags | GdObject class and methods
tags-method | GdObject class and methods
tags-method | ImageMap class and methods
tail-method | DisplayPars class and method
to | Data sets
transcript | GeneRegionTrack class and methods
transcript-method | GeneRegionTrack class and methods
transcript<- | GeneRegionTrack class and methods
transcript<--method | GeneRegionTrack class and methods
twoGroups | Data sets

## -- U --

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

## -- V --

values-method | AlignmentsTrack class and methods
values-method | DataTrack class and methods
values-method | GenomeAxisTrack class and methods
values-method | RangeTrack class and methods
values<--method | DataTrack class and methods

## -- W --

width-method | GenomeAxisTrack class and methods
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 --

[ | RangeTrack class and methods
[-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE)
[-method | AlignmentsTrack class and methods
[-method | DataTrack class and methods
[-method | GenomeAxisTrack class and methods
[-method | IdeogramTrack class and methods
[-method | RangeTrack class and methods
[-method | StackedTrack class and methods