ivanek/Gviz
Plotting data and annotation information along genomic coordinates

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Search the ivanek/Gviz package
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457
Source code
62
Man pages
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ivanek/Gviz: Plotting data and annotation information along genomic coordinates
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API

API for ivanek/Gviz
Plotting data and annotation information along genomic coordinates

Global functions
.DisplayPars Man page
.SequenceTrack Source code
.addFeatInfo Source code
.aggregator Source code
.alpha Source code
.annotationTrackInfo Source code
.arrowBar Source code
.barsAndLabels Source code
.bmGuid Source code
.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
.collapseAnnotation Source code
.collectSchemes Source code
.computeAlignments Source code
.computeGroupRange Source code
.convert.summarizedJunctions.to.sashimi.junctions Source code
.covDefault Source code
.create.summarizedJunctions.for.sashimi.junctions Source code
.deepCopyPars Source code
.defaultRange Source code
.defaultVarMap Source code
.doCache Source code
.dpOrDefault Source code
.dpOrDefaultFont Source code
.expBed Source code
.expLabel Source code
.extreme Source code
.fetchBMData Source code
.fileExtension Source code
.fillWithDefaults Source code
.filledArrow Source code
.filledBoxes Source code
.findMismatches Source code
.fontGp Source code
.genome2Dataset Source code
.getAnn Source code
.getBMFeatureMap Source code
.getBioColorIdeo Source code
.getBiomart Source code
.getBiotypeColor Source code
.getCovars Source code
.getGenomeFromGRange Source code
.getImageMap Source code
.getPlottingFeatures Source code
.getStringDims Source code
.handleComposite Source code
.import.2bit Source code
.import.bam Source code
.import.bam.alignments Source code
.import.bw Source code
.import.fasta Source code
.import.gff3 Source code
.legendInfo Source code
.makeParMapping Source code
.missingToNull Source code
.moreInd Source code
.myFindOverlaps Source code
.needsAxis Source code
.needsStacking Source code
.needsTitle Source code
.onLoad Source code
.panel.bwplot Source code
.panel.mountain Source code
.panel.polygon Source code
.prepareDtData Source code
.providerVersion Source code
.pxResolution Source code
.ranges2ga Source code
.recChromosome Source code
.referenceTrackInfo Source code
.registerImportFun Source code
.resize Source code
.resolveColMapping Source code
.roundedCap Source code
.runaggregator Source code
.sequenceTrackInfo Source code
.setAnn Source code
.setupTextSize Source code
.strandName Source code
.supportsAlpha Source code
.ticks Source code
.transcriptsAreCollapsed Source code
.ucsc2Ensembl Source code
.updateDp Source code
.updateObj Source code
.updatePars Source code
.verticalSpace Source code
.whichStrand Source code
.z2icol Source code
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-class Man page
GeneRegionTrack Man page Source code
GeneRegionTrack-class Man page
GenomeAxisTrack Man page Source code
GenomeAxisTrack-class Man page
Gviz-defunct Man page
Gviz-deprecated 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-class Man page
OverlayTrack Man page Source code
OverlayTrack-class Man page
RNASequenceTrack Man page Source code
RangeTrack-class Man page
ReferenceAlignmentsTrack-class Man page
ReferenceAnnotationTrack-class Man page
ReferenceDataTrack-class Man page
ReferenceGeneRegionTrack-class Man page
ReferenceSequenceTrack-class Man page
ReferenceTrack-class Man page
SequenceBSgenomeTrack-class Man page
SequenceDNAStringSetTrack-class Man page
SequenceRNAStringSetTrack-class Man page
SequenceTrack Man page Source code
SequenceTrack-class Man page
StackedTrack-class Man page
UcscTrack Man page Source code
[,DataTrack,ANY,ANY,ANY-method Man page
[,GenomeAxisTrack,ANY,ANY,ANY-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
[,StackedTrack,ANY,ANY,ANY-method Man page
addScheme Man page 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
biomTrack Man page
biomTrack2 Man page
bmTrack Man page
bmt Man page
chromosome Man page
chromosome,GdObject-method Man page
chromosome,OverlayTrack-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
collapseTrack,AnnotationTrack-method Man page
collapseTrack,DataTrack-method Man page
collapseTrack,GenomeAxisTrack-method Man page
collapsing Man page
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
coords Man page
coords,GdObject-method Man page
coords,ImageMap-method Man page
coords,NULL-method Man page
cpgIslands Man page
ctrack Man page
cyp2b10 Man page
datasets Man page
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
drawAxis 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,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 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
exportTracks Man page 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
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,GdObject-method Man page
genome,RangeTrack-method Man page
genome,SequenceTrack-method Man page
genome<-,GdObject-method Man page
genome<-,IdeogramTrack-method Man page
genome<-,RangeTrack-method Man page
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
getScheme Man page 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
iTrack 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
imageMap<- Man page
imageMap<-,GdObject,ImageMapOrNULL-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,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,SequenceRNAStringSetTrack-method Man page
initialize,SequenceTrack-method Man page
initialize,StackedTrack-method Man page
itrack Man page
knownGenes Man page
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
max,RangeTrack-method Man page
min,RangeTrack-method Man page
names,GdObject-method Man page
names<-,GdObject,character-method Man page
plotTracks Man page Source code
position Man page
position,IdeogramTrack-method Man page
position,RangeTrack-method Man page
range,GenomeAxisTrack-method Man page
range,RangeTrack-method Man page
ranges,GenomeAxisTrack-method Man page
ranges,RangeTrack-method Man page
refGenes Man page
seqinfo,RangeTrack-method Man page
seqlevels,RangeTrack-method Man page
seqlevels,SequenceBSgenomeTrack-method Man page
seqlevels,SequenceTrack-method Man page
seqnames,RangeTrack-method Man page
seqnames,SequenceBSgenomeTrack-method Man page
seqnames,SequenceTrack-method Man page
setCoverage 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 Man page
setStacks,AlignmentsTrack-method Man page
setStacks,AnnotationTrack-method Man page
setStacks,GdObject-method Man page
setStacks,HighlightTrack-method Man page
setStacks,OverlayTrack-method Man page
setStacks,StackedTrack-method Man page
settings 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,InferredDisplayPars-method Man page
show,OverlayTrack-method Man page
show,ReferenceAlignmentsTrack-method Man page
show,ReferenceAnnotationTrack-method Man page
show,ReferenceDataTrack-method Man page
show,ReferenceGeneRegionTrack-method Man page
show,ReferenceSequenceTrack-method Man page
show,SequenceBSgenomeTrack-method Man page
show,SequenceDNAStringSetTrack-method Man page
show,SequenceRNAStringSetTrack-method Man page
snpLocations Man page
split,DataTrack,ANY-method Man page
split,RangeTrack,ANY-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<-,RangeTrack,ANY-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
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
to Man page
transcript Man page
transcript,GeneRegionTrack-method Man page
transcript<- Man page
transcript<-,GeneRegionTrack,character-method Man page
twoGroups Man page
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
vpLocation 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
ivanek/Gviz documentation built on Nov. 20, 2023, 8:16 p.m.

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