Plotting data and annotation information along genomic coordinates


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Documentation for package ‘Gviz’ version 1.44.1

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