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initialize(<AlignmentsTrack>) initialize(<ReferenceAlignmentsTrack>) AlignmentsTrack() values(<AlignmentsTrack>) `chromosome<-`(<AlignmentsTrack>) stacks(<AlignmentsTrack>) setStacks(<AlignmentsTrack>) subset(<AlignmentsTrack>) subset(<ReferenceAlignmentsTrack>) drawGrid(<AlignmentsTrack>) drawAxis(<AlignmentsTrack>) drawGD(<AlignmentsTrack>) show(<AlignmentsTrack>) show(<ReferenceAlignmentsTrack>)
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AlignmentsTrack class and methods |
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initialize(<BiomartGeneRegionTrack>) BiomartGeneRegionTrack() subset(<BiomartGeneRegionTrack>)
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BiomartGeneRegionTrack class and methods |
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initialize(<CustomTrack>) CustomTrack() drawGD(<CustomTrack>) show(<CustomTrack>)
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CustomTrack class and methods |
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DetailsAnnotationTrack() initialize(<DetailsAnnotationTrack>) drawGD(<DetailsAnnotationTrack>)
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The DetailsAnnotationTrack class directly extends AnnotationTrack |
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DisplayPars() getPar() displayPars() as.list(<DisplayPars>) setPar() `displayPars<-`() show(<DisplayPars>) as.list(<InferredDisplayPars>) show(<InferredDisplayPars>) availableDisplayPars()
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DisplayPars: A class to control the plotting parameters for GdObjects |
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initialize(<GeneRegionTrack>) initialize(<ReferenceGeneRegionTrack>) GeneRegionTrack() gene(<GeneRegionTrack>) `gene<-`(<GeneRegionTrack>,<character>) symbol(<GeneRegionTrack>) `symbol<-`(<GeneRegionTrack>,<character>) transcript(<GeneRegionTrack>) `transcript<-`(<GeneRegionTrack>,<character>) exon(<GeneRegionTrack>) `exon<-`(<GeneRegionTrack>,<character>) group(<GeneRegionTrack>) `group<-`(<GeneRegionTrack>,<character>) identifier(<GeneRegionTrack>) `identifier<-`(<GeneRegionTrack>,<character>) subset(<ReferenceGeneRegionTrack>) drawGD(<GeneRegionTrack>) show(<GeneRegionTrack>) show(<ReferenceGeneRegionTrack>)
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GeneRegionTrack class and methods |
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Gviz-defunct
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Defunct functions in package Gviz |
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Gviz-deprecated
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Deprecated functions in package Gviz |
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initialize(<HighlightTrack>) HighlightTrack() `displayPars<-`(<HighlightTrack>,<list>) length(<HighlightTrack>) `chromosome<-`(<HighlightTrack>) setStacks(<HighlightTrack>) consolidateTrack(<HighlightTrack>) subset(<HighlightTrack>) show(<HighlightTrack>)
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HighlightTrack class and methods |
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initialize(<IdeogramTrack>) IdeogramTrack() start(<IdeogramTrack>) `start<-`(<IdeogramTrack>) end(<IdeogramTrack>) `end<-`(<IdeogramTrack>) width(<IdeogramTrack>) `width<-`(<IdeogramTrack>) length(<IdeogramTrack>) `chromosome<-`(<IdeogramTrack>) `genome<-`(<IdeogramTrack>) `[`(<IdeogramTrack>,<ANY>,<ANY>,<ANY>) position(<IdeogramTrack>) drawGD(<IdeogramTrack>) show(<IdeogramTrack>)
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IdeogramTrack class and methods |
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drawAxis(<NumericTrack>) drawGrid(<NumericTrack>)
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NumericTrack class and methods |
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initialize(<RangeTrack>) ranges(<RangeTrack>) `ranges<-`(<RangeTrack>) range(<RangeTrack>) seqnames(<RangeTrack>) seqlevels(<RangeTrack>) seqinfo(<RangeTrack>) genome(<RangeTrack>) `genome<-`(<RangeTrack>) chromosome(<RangeTrack>) `chromosome<-`(<RangeTrack>) start(<RangeTrack>) `start<-`(<RangeTrack>) end(<RangeTrack>) `end<-`(<RangeTrack>) width(<RangeTrack>) `width<-`(<RangeTrack>) min(<RangeTrack>) max(<RangeTrack>) length(<RangeTrack>) strand(<RangeTrack>) `strand<-`(<RangeTrack>,<ANY>) position(<RangeTrack>) `[`(<RangeTrack>,<ANY>,<ANY>,<ANY>) subset(<RangeTrack>) split(<RangeTrack>,<ANY>) values(<RangeTrack>) feature(<RangeTrack>) `feature<-`(<RangeTrack>,<character>) consolidateTrack(<RangeTrack>)
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RangeTrack class and methods |
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availableDefaultMapping() initialize(<ReferenceTrack>)
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ReferenceTrack class and methods |
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initialize(<SequenceBSgenomeTrack>)
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The BSgenome-based version of the SequenceTrack class |
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initialize(<SequenceDNAStringSetTrack>)
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The DNAStringSet-based version of the SequenceTrack class |
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initialize(<SequenceRNAStringSetTrack>)
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The RNAStringSet-based version of the SequenceTrack class |
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initialize(<SequenceTrack>) SequenceTrack() RNASequenceTrack() seqnames(<SequenceTrack>) seqnames(<SequenceBSgenomeTrack>) seqlevels(<SequenceTrack>) seqlevels(<SequenceBSgenomeTrack>) start(<SequenceTrack>) end(<SequenceTrack>) width(<SequenceTrack>) length(<SequenceTrack>) subseq(<SequenceTrack>) subseq(<ReferenceSequenceTrack>) chromosome(<SequenceTrack>) `chromosome<-`(<SequenceTrack>) genome(<SequenceTrack>) consolidateTrack(<SequenceTrack>) drawGD(<SequenceTrack>) show(<SequenceBSgenomeTrack>) show(<SequenceDNAStringSetTrack>) show(<SequenceRNAStringSetTrack>) show(<ReferenceSequenceTrack>)
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SequenceTrack class and methods |
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initialize(<StackedTrack>) stacking(<StackedTrack>) `stacking<-`(<StackedTrack>,<character>) stacks(<StackedTrack>) setStacks(<StackedTrack>) consolidateTrack(<StackedTrack>) `[`(<StackedTrack>,<ANY>,<ANY>,<ANY>) subset(<StackedTrack>) drawGD(<StackedTrack>)
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StackedTrack class and methods |
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UcscTrack()
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Meta-constructor for Gviz tracks fetched directly from the various UCSC data sources |
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collapsing
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Dynamic content based on the available resolution |
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datasets bmTrack cyp2b10 idTrack biomTrack biomTrack2 cpgIslands axTrack conservation ensGenes denseAnnTrack geneModels iTrack itrack idxTrack ideoTrack twoGroups from gcContent knownGenes refGenes snpLocations to ctrack geneDetails dtHoriz bmt
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Data sets |
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exportTracks()
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Export Gviz tracks into an annotation file representation |
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grouping
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Grouping of annotation features |
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plotTracks()
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The main plotting function for one or several Gviz tracks |
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settings addScheme getScheme
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Setting display parameters to control the look and feel of the plots |