Plotting data and annotation information along genomic coordinates

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Documentation for package ‘Gviz’ version 1.53.0

• 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