API for Gviz
Plotting data and annotation information along genomic coordinates

Global functions
AlignedReadTrack Man page Source code
AlignedReadTrack-class Man page
AlignmentsTrack Man page Source code
AlignmentsTrack-class Man page
AnnotationTrack Man page Source code
AnnotationTrack-class Man page
BiomartGeneRegionTrack Man page Source code
BiomartGeneRegionTrack-class Man page
CustomTrack Man page Source code
CustomTrack-class Man page
DataTrack Man page Source code
DataTrack-class Man page
DetailsAnnotationTrack Man page Source code
DetailsAnnotationTrack-class Man page
DisplayPars Man page Source code
DisplayPars-class Man page
GdObject Man page
GdObject-class Man page
GeneRegionTrack Man page Source code
GeneRegionTrack-class Man page
GenomeAxisTrack Man page Source code
GenomeAxisTrack-class Man page
HighlightTrack Man page Source code
HighlightTrack-class Man page
IdeogramTrack Man page Source code
IdeogramTrack-class Man page
ImageMap Source code
ImageMap-class Man page
NumericTrack Man page
NumericTrack-class Man page
OverlayTrack Man page Source code
OverlayTrack-class Man page
RangeTrack Man page
RangeTrack-class Man page
ReferenceTrack Man page
ReferenceTrack-class Man page
SequenceTrack Man page Source code
SequenceTrack-class Man page
StackedTrack Man page
StackedTrack-class Man page
UcscTrack Man page Source code
[ Man page
[,AlignedReadTrack,ANY,ANY,ANY-method Man page
[,AlignedReadTrack,ANY,ANY-method Man page
[,AlignedReadTrack-method Man page
[,AlignmentsTrack,ANY,ANY-method Man page
[,DataTrack,ANY,ANY,ANY-method Man page
[,DataTrack,ANY,ANY-method Man page
[,DataTrack-method Man page
[,GenomeAxisTrack,ANY,ANY,ANY-method Man page
[,GenomeAxisTrack,ANY,ANY-method Man page
[,GenomeAxisTrack-method Man page
[,IdeogramTrack,ANY,ANY,ANY-method Man page
[,IdeogramTrack,ANY,ANY-method Man page
[,IdeogramTrack-method Man page
[,RangeTrack,ANY,ANY,ANY-method Man page
[,RangeTrack,ANY,ANY-method Man page
[,RangeTrack-method Man page
[,StackedTrack,ANY,ANY,ANY-method Man page
[,StackedTrack,ANY,ANY-method Man page
addFeatInfo Source code
addScheme Man page Source code
aggregator Source code
alpha Source code
annotationTrackInfo Source code
arrowBar Source code
as.list,DisplayPars-method Man page
as.list,InferredDisplayPars-method Man page
availableDefaultMapping Man page Source code
availableDisplayPars Man page Source code
axTrack Man page
barsAndLabels Source code
biomTrack Man page
bmGuid Source code
bmTrack Man page
bmt Man page
box2Ellipse Source code
boxes Source code
buildArgsDf Source code
cacheGenomes Source code
cacheMartData Source code
cacheTracks Source code
checkClass Source code
chooseFace Source code
chrName Source code
chromosome Man page
chromosome,GdObject-method Man page
chromosome,RangeTrack-method Man page
chromosome,SequenceTrack-method Man page
chromosome<- Man page
chromosome<-,AlignmentsTrack-method Man page
chromosome<-,GdObject-method Man page
chromosome<-,HighlightTrack-method Man page
chromosome<-,IdeogramTrack-method Man page
chromosome<-,OverlayTrack-method Man page
chromosome<-,RangeTrack-method Man page
chromosome<-,SequenceTrack-method Man page
clearSessionCache Man page Source code
coerce,AnnotationTrack,UCSCData-method Man page
coerce,DNAString,Rle-method Man page
coerce,DataTrack,data.frame-method Man page
coerce,DisplayPars,list-method Man page
coerce,GRanges,AnnotationTrack-method Man page
coerce,GRanges,DataTrack-method Man page
coerce,GRanges,GeneRegionTrack-method Man page
coerce,GRangesList,AnnotationTrack-method Man page
coerce,GRangesList,GeneRegionTrack-method Man page
coerce,GeneRegionTrack,UCSCData-method Man page
coerce,InferredDisplayPars,list-method Man page
coerce,RangeTrack,data.frame-method Man page
coerce,TxDb,GeneRegionTrack-method Man page
collapseAnnotation Source code
collapseTrack,AnnotationTrack-method Man page
collapseTrack,DataTrack-method Man page
collapseTrack,GeneRegionTrack-method Man page
collapseTrack,GenomeAxisTrack-method Man page
collapsing Man page
collectSchemes Source code
computeAlignments Source code
computeGroupRange Source code
conservation Man page
consolidateTrack Man page
consolidateTrack,AnnotationTrack-method Man page
consolidateTrack,GdObject-method Man page
consolidateTrack,HighlightTrack-method Man page
consolidateTrack,OverlayTrack-method Man page
consolidateTrack,RangeTrack-method Man page
consolidateTrack,SequenceTrack-method Man page
consolidateTrack,StackedTrack-method Man page
convert.summarizedJunctions.to.sashimi.junctions Source code
coords Man page
coords,GdObject-method Man page
coords,ImageMap-method Man page
coords,NULL-method Man page
covDefault Source code
coverage,AlignedReadTrack-method Man page
coverage,AlignmentsTrack-method Man page
cpgIslands Man page
create.summarizedJunctions.for.sashimi.junctions Source code
ctrack Man page
cyp2b10 Man page
deepCopyPars Source code
defaultRange Source code
defaultVarMap Source code
denseAnnTrack Man page
devDims Source code
devRes Source code
displayPars Man page
displayPars,DisplayPars,character-method Man page
displayPars,DisplayPars,missing-method Man page
displayPars,GdObject,character-method Man page
displayPars,GdObject,missing-method Man page
displayPars<- Man page
displayPars<-,DisplayPars,list-method Man page
displayPars<-,GdObject,list-method Man page
displayPars<-,HighlightTrack,list-method Man page
displayPars<-,OverlayTrack,list-method Man page
doCache Source code
dpOrDefault Source code
dpOrDefaultFont Source code
drawAxis Man page
drawAxis,AlignedReadTrack-method Man page
drawAxis,AlignmentsTrack-method Man page
drawAxis,DataTrack-method Man page
drawAxis,GdObject-method Man page
drawAxis,NumericTrack-method Man page
drawGD Man page
drawGD,AlignedReadTrack-method Man page
drawGD,AlignmentsTrack-method Man page
drawGD,AnnotationTrack-method Man page
drawGD,CustomTrack-method Man page
drawGD,DataTrack-method Man page
drawGD,DetailsAnnotationTrack-method Man page
drawGD,GeneRegionTrack-method Man page
drawGD,GenomeAxisTrack-method Man page
drawGD,IdeogramTrack-method Man page
drawGD,OverlayTrack-method Man page
drawGD,SequenceTrack-method Man page
drawGD,StackedTrack-method Man page
drawGrid,AlignedReadTrack-method Man page
drawGrid,AnnotationTrack-method Man page
drawGrid,GdObject-method Man page
drawGrid,NumericTrack-method Man page
dtHoriz Man page
end,GenomeAxisTrack-method Man page
end,IdeogramTrack-method Man page
end,RangeTrack-method Man page
end,SequenceTrack-method Man page
end<-,GenomeAxisTrack-method Man page
end<-,IdeogramTrack-method Man page
end<-,RangeTrack-method Man page
ensGenes Man page
exon Man page
exon,GeneRegionTrack-method Man page
exon<- Man page
exon<-,GeneRegionTrack,character-method Man page
expBed Source code
expLabel Source code
exportTracks Man page Source code
extreme Source code
feature Man page
feature,DataTrack-method Man page
feature,RangeTrack-method Man page
feature<- Man page
feature<-,DataTrack,character-method Man page
feature<-,RangeTrack,character-method Man page
fetchBMData Source code
fileExtension Source code
fillWithDefaults Source code
filledArrow Source code
filledBoxes Source code
findMismatches Source code
fontGp Source code
from Man page
gcContent Man page
gene Man page
gene,GeneRegionTrack-method Man page
gene<- Man page
gene<-,GeneRegionTrack,character-method Man page
geneDetails Man page
geneModels Man page
genome,RangeTrack-method Man page
genome,SequenceTrack-method Man page
genome2Dataset Source code
genome<-,GdObject-method Man page
genome<-,IdeogramTrack-method Man page
genome<-,RangeTrack-method Man page
getAnn Source code
getBMFeatureMap Source code
getBioColorIdeo Source code
getBiomart Source code
getBiotypeColor Source code
getCovars Source code
getGenomeFromGRange Source code
getImageMap Source code
getPar Man page
getPar,DisplayPars,character-method Man page
getPar,DisplayPars,missing-method Man page
getPar,GdObject,character-method Man page
getPar,GdObject,missing-method Man page
getPlottingFeatures Source code
getScheme Man page Source code
getStringDims Source code
group Man page
group,AnnotationTrack-method Man page
group,GdObject-method Man page
group,GeneRegionTrack-method Man page
group<- Man page
group<-,AnnotationTrack,character-method Man page
group<-,GeneRegionTrack,character-method Man page
grouping Man page
handleComposite Source code
head,InferredDisplayPars-method Man page
idTrack Man page
identifier Man page
identifier,AnnotationTrack-method Man page
identifier,GeneRegionTrack-method Man page
identifier<- Man page
identifier<-,AnnotationTrack,character-method Man page
identifier<-,GeneRegionTrack,character-method Man page
ideoTrack Man page
idxTrack Man page
imageMap Man page
imageMap,GdObject-method Man page
initialize,AlignedReadTrack-method Man page
initialize,AlignmentsTrack-method Man page
initialize,AnnotationTrack-method Man page
initialize,BiomartGeneRegionTrack-method Man page
initialize,CustomTrack-method Man page
initialize,DataTrack-method Man page
initialize,DetailsAnnotationTrack-method Man page
initialize,DisplayPars-method Man page
initialize,GdObject-method Man page
initialize,GeneRegionTrack-method Man page
initialize,GenomeAxisTrack-method Man page
initialize,HighlightTrack-method Man page
initialize,IdeogramTrack-method Man page
initialize,OverlayTrack-method Man page
initialize,RangeTrack-method Man page
initialize,ReferenceAlignmentsTrack-method Man page
initialize,ReferenceAnnotationTrack-method Man page
initialize,ReferenceDataTrack-method Man page
initialize,ReferenceGeneRegionTrack-method Man page
initialize,ReferenceSequenceTrack-method Man page
initialize,ReferenceTrack-method Man page
initialize,SequenceBSgenomeTrack-method Man page
initialize,SequenceDNAStringSetTrack-method Man page
initialize,SequenceTrack-method Man page
initialize,StackedTrack-method Man page
isActiveSeq,RangeTrack-method Man page
isActiveSeq<-,GdObject-method Man page
itrack Man page
knownGenes Man page
legendInfo Source code
length,GenomeAxisTrack-method Man page
length,HighlightTrack-method Man page
length,IdeogramTrack-method Man page
length,OverlayTrack-method Man page
length,RangeTrack-method Man page
length,SequenceTrack-method Man page
makeParMapping Source code
max,RangeTrack-method Man page
min,RangeTrack-method Man page
missingToNull Source code
moreInd Source code
mport.2bit Source code
mport.bam Source code
mport.bam.alignments Source code
mport.bw Source code
mport.fasta Source code
mport.gff3 Source code
myFindOverlaps Source code
names,GdObject-method Man page
names<-,GdObject,character-method Man page
needsAxis Source code
needsStacking Source code
needsTitle Source code
onLoad Source code
panel.bwplot Source code
panel.mountain Source code
panel.polygon Source code
plotTracks Man page Source code
position Man page
position,IdeogramTrack-method Man page
position,RangeTrack-method Man page
prepareDtData Source code
pxResolution Source code
range Man page
range,DataTrack-method Man page
range,GenomeAxisTrack-method Man page
range,RangeTrack-method Man page
ranges,GenomeAxisTrack-method Man page
ranges,RangeTrack-method Man page
ranges<-,GenomeAxisTrack-method Man page
ranges<-,RangeTrack-method Man page
recChromosome Source code
refGenes Man page
referenceTrackInfo Source code
registerImportFun Source code
resize Source code
resolveColMapping Source code
roundedCap Source code
score,DataTrack-method Man page
seqinfo,RangeTrack-method Man page
seqlevels,RangeTrack-method Man page
seqlevels,SequenceBSgenomeTrack-method Man page
seqlevels,SequenceDNAStringSetTrack-method Man page
seqnames,RangeTrack-method Man page
seqnames,SequenceBSgenomeTrack-method Man page
seqnames,SequenceDNAStringSetTrack-method Man page
sequenceTrackInfo Source code
setAnn Source code
setCoverage,AlignedReadTrack-method Man page
setPar Man page
setPar,DisplayPars,character-method Man page
setPar,DisplayPars,list-method Man page
setPar,GdObject,character-method Man page
setPar,GdObject,list-method Man page
setStacks,AnnotationTrack-method Man page
setStacks,HighlightTrack-method Man page
setStacks,OverlayTrack-method Man page
setStacks,StackedTrack-method Man page
settings Man page
setupTextSize Source code
show,AlignedReadTrack-method Man page
show,AlignmentsTrack-method Man page
show,AnnotationTrack-method Man page
show,CustomTrack-method Man page
show,DataTrack-method Man page
show,DisplayPars-method Man page
show,GeneRegionTrack-method Man page
show,GenomeAxisTrack-method Man page
show,HighlightTrack-method Man page
show,IdeogramTrack-method Man page
show,OverlayTrack-method Man page
show,ReferenceAnnotationTrack-method Man page
show,ReferenceDataTrack-method Man page
show,ReferenceGeneRegionTrack-method Man page
snpLocations Man page
split,AlignedReadTrack,ANY-method Man page
split,AlignedReadTrack-method Man page
split,DataTrack,ANY-method Man page
split,DataTrack-method Man page
split,RangeTrack,ANY-method Man page
split,RangeTrack-method Man page
stacking Man page
stacking,StackedTrack-method Man page
stacking<- Man page
stacking<-,StackedTrack,character-method Man page
stacks Man page
stacks,AlignmentsTrack-method Man page
stacks,StackedTrack-method Man page
start,GenomeAxisTrack-method Man page
start,IdeogramTrack-method Man page
start,RangeTrack-method Man page
start,SequenceTrack-method Man page
start<-,GenomeAxisTrack-method Man page
start<-,IdeogramTrack-method Man page
start<-,RangeTrack-method Man page
strand,DataTrack-method Man page
strand,GenomeAxisTrack-method Man page
strand,RangeTrack-method Man page
strand<-,DataTrack,ANY-method Man page
strand<-,DataTrack-method Man page
strand<-,RangeTrack,ANY-method Man page
strandName Source code
subseq,ReferenceSequenceTrack-method Man page
subseq,SequenceTrack-method Man page
subset,AlignedReadTrack-method Man page
subset,AlignmentsTrack-method Man page
subset,AnnotationTrack-method Man page
subset,BiomartGeneRegionTrack-method Man page
subset,DataTrack-method Man page
subset,GdObject-method Man page
subset,GenomeAxisTrack-method Man page
subset,HighlightTrack-method Man page
subset,IdeogramTrack-method Man page
subset,OverlayTrack-method Man page
subset,RangeTrack-method Man page
subset,ReferenceAlignmentsTrack-method Man page
subset,ReferenceAnnotationTrack-method Man page
subset,ReferenceDataTrack-method Man page
subset,ReferenceGeneRegionTrack-method Man page
subset,StackedTrack-method Man page
supportsAlpha Source code
symbol Man page
symbol,GeneRegionTrack-method Man page
symbol<- Man page
symbol<-,GeneRegionTrack,character-method Man page
tags Man page
tags,GdObject-method Man page
tags,ImageMap-method Man page
tags,NULL-method Man page
tail,InferredDisplayPars-method Man page
ticks Source code
to Man page
transcript Man page
transcript,GeneRegionTrack-method Man page
transcript<- Man page
transcript<-,GeneRegionTrack,character-method Man page
transcriptsAreCollapsed Source code
twoGroups Man page
ucsc2Ensembl Source code
ucscUrl Source code
updateDp Source code
updateObj Source code
updatePars Source code
values,AlignmentsTrack-method Man page
values,DataTrack-method Man page
values,GenomeAxisTrack-method Man page
values,RangeTrack-method Man page
values<-,DataTrack-method Man page
verticalSpace Source code
vpLocation Source code
whichStrand Source code
width,GenomeAxisTrack-method Man page
width,IdeogramTrack-method Man page
width,RangeTrack-method Man page
width,SequenceTrack-method Man page
width<-,IdeogramTrack-method Man page
width<-,RangeTrack-method Man page
z2icol Source code
Gviz documentation built on Nov. 1, 2018, 5 a.m.