Plotting data and annotation information along genomic coordinates


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Documentation for package ‘Gviz’ version 1.18.0

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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 HighlightTrack class and methods
chromosome<--method IdeogramTrack class and methods
chromosome<--method OverlayTrack 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
CustomTrack CustomTrack class and methods
CustomTrack-class CustomTrack class and methods
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
displayPars<--method HighlightTrack class and methods
displayPars<--method OverlayTrack 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 CustomTrack 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 CustomTrack 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 CustomTrack 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 BiomartGeneRegionTrack 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