Package: Gviz 1.51.0
Robert Ivanek
Gviz: Plotting data and annotation information along genomic coordinates
Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.
Authors:
Gviz_1.51.0.tar.gz
Gviz_1.51.0.zip(r-4.5)Gviz_1.51.0.zip(r-4.4)Gviz_1.51.0.zip(r-4.3)
Gviz_1.51.0.tgz(r-4.4-any)Gviz_1.51.0.tgz(r-4.3-any)
Gviz_1.51.0.tar.gz(r-4.5-noble)Gviz_1.51.0.tar.gz(r-4.4-noble)
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Gviz.pdf |Gviz.html✨
Gviz/json (API)
NEWS
| # Install 'Gviz' in R: |
| install.packages('Gviz', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ivanek/gviz/issues
- axTrack - Data sets
- biomTrack - Data sets
- biomTrack2 - Data sets
- bmTrack - Data sets
- bmt - Data sets
- conservation - Data sets
- cpgIslands - Data sets
- cpgIslands - Data sets
- ctrack - Data sets
- cyp2b10 - Data sets
- denseAnnTrack - Data sets
- dtHoriz - Data sets
- ensGenes - Data sets
- from - Data sets
- gcContent - Data sets
- geneDetails - Data sets
- geneModels - Data sets
- idTrack - Data sets
- ideoTrack - Data sets
- idxTrack - Data sets
- itrack - Data sets
- knownGenes - Data sets
- refGenes - Data sets
- snpLocations - Data sets
- to - Data sets
- twoGroups - Data sets
On BioConductor:Gviz-1.49.0(bioc 3.20)Gviz-1.48.0(bioc 3.19)
visualizationmicroarraysequencing
Last updated 14 days agofrom:60a0f4aec1. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | OK | Oct 31 2024 |
| R-4.4-mac | OK | Oct 31 2024 |
| R-4.3-win | OK | Oct 31 2024 |
| R-4.3-mac | OK | Oct 31 2024 |
Exports:.chrName.DisplayPars.doCacheaddSchemeAlignmentsTrackAnnotationTrackas.listavailableDefaultMappingavailableDisplayParsBiomartGeneRegionTrackchromosomechromosome<-clearSessionCacheconsolidateTrackcoordsCustomTrackDataTrackDetailsAnnotationTrackdisplayParsDisplayParsdisplayPars<-drawAxisdrawGDendend<-exonexon<-exportTracksfeaturefeature<-genegene<-GeneRegionTrackgenomegenome<-GenomeAxisTrackgetPargetSchemegroupgroup<-HighlightTrackidentifieridentifier<-IdeogramTrackimageMapimageMap<-initializeOverlayTrackplotTrackspositionRNASequenceTrackseqinfoseqlevelsseqnamesSequenceTracksetCoveragesetParsetStacksshowsplitstackingstacking<-stacksstartstart<-strandstrand<-subsetsymbolsymbol<-tagstranscripttranscript<-UcscTrackvaluesvalues<-widthwidth<-
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| AlignmentsTrack class and methods | AlignmentsTrack AlignmentsTrack-class chromosome<-,AlignmentsTrack-method drawAxis,AlignmentsTrack-method drawGD,AlignmentsTrack-method initialize,AlignmentsTrack-method initialize,ReferenceAlignmentsTrack-method ReferenceAlignmentsTrack-class setStacks,AlignmentsTrack-method show,AlignmentsTrack-method show,ReferenceAlignmentsTrack-method stacks,AlignmentsTrack-method subset,AlignmentsTrack-method subset,ReferenceAlignmentsTrack-method values,AlignmentsTrack-method |
| ReferenceTrack class and methods | availableDefaultMapping initialize,ReferenceTrack-method ReferenceTrack-class |
| BiomartGeneRegionTrack class and methods | BiomartGeneRegionTrack BiomartGeneRegionTrack-class initialize,BiomartGeneRegionTrack-method subset,BiomartGeneRegionTrack-method |
| Dynamic content based on the available resolution | collapsing |
| CustomTrack class and methods | CustomTrack CustomTrack-class drawGD,CustomTrack-method initialize,CustomTrack-method show,CustomTrack-method |
| Data sets | axTrack biomTrack biomTrack2 bmt bmTrack conservation cpgIslands ctrack cyp2b10 datasets denseAnnTrack dtHoriz ensGenes from gcContent geneDetails geneModels ideoTrack idTrack idxTrack iTrack itrack knownGenes refGenes snpLocations to twoGroups |
| DisplayPars: A class to control the plotting parameters for GdObjects | .DisplayPars as.list,DisplayPars-method as.list,InferredDisplayPars-method availableDisplayPars DisplayPars displayPars displayPars,DisplayPars,character-method displayPars,DisplayPars,missing-method DisplayPars-class displayPars<- displayPars<-,DisplayPars,list-method getPar getPar,DisplayPars,character-method getPar,DisplayPars,missing-method setPar setPar,DisplayPars,character-method setPar,DisplayPars,list-method show,DisplayPars-method show,InferredDisplayPars-method |
| Export Gviz tracks into an annotation file representation. | exportTracks |
| GeneRegionTrack class and methods | drawGD,GeneRegionTrack-method exon,GeneRegionTrack-method exon<-,GeneRegionTrack,character-method gene,GeneRegionTrack-method gene<-,GeneRegionTrack,character-method GeneRegionTrack GeneRegionTrack-class group,GeneRegionTrack-method group<-,GeneRegionTrack,character-method identifier,GeneRegionTrack-method identifier<-,GeneRegionTrack,character-method initialize,GeneRegionTrack-method initialize,ReferenceGeneRegionTrack-method ReferenceGeneRegionTrack-class show,GeneRegionTrack-method show,ReferenceGeneRegionTrack-method subset,ReferenceGeneRegionTrack-method symbol,GeneRegionTrack-method symbol<-,GeneRegionTrack,character-method transcript,GeneRegionTrack-method transcript<-,GeneRegionTrack,character-method |
| Grouping of annotation features | grouping |
| Defunct functions in package 'Gviz' | Gviz-defunct |
| Deprecated functions in package 'Gviz' | Gviz-deprecated |
| HighlightTrack class and methods | chromosome<-,HighlightTrack-method consolidateTrack,HighlightTrack-method displayPars<-,HighlightTrack,list-method HighlightTrack HighlightTrack-class initialize,HighlightTrack-method length,HighlightTrack-method setStacks,HighlightTrack-method show,HighlightTrack-method subset,HighlightTrack-method |
| IdeogramTrack class and methods | chromosome<-,IdeogramTrack-method drawGD,IdeogramTrack-method end,IdeogramTrack-method end<-,IdeogramTrack-method genome<-,IdeogramTrack-method IdeogramTrack IdeogramTrack-class initialize,IdeogramTrack-method length,IdeogramTrack-method position,IdeogramTrack-method show,IdeogramTrack-method start,IdeogramTrack-method start<-,IdeogramTrack-method subset,IdeogramTrack-method width,IdeogramTrack-method width<-,IdeogramTrack-method [,IdeogramTrack,ANY,ANY,ANY-method [,IdeogramTrack,ANY,ANY-method [,IdeogramTrack-method |
| NumericTrack class and methods | drawAxis,NumericTrack-method drawGrid,NumericTrack-method NumericTrack-class |
| The main plotting function for one or several Gviz tracks. | plotTracks |
| RangeTrack class and methods | chromosome,RangeTrack-method chromosome<-,RangeTrack-method consolidateTrack,RangeTrack-method end,RangeTrack-method end<-,RangeTrack-method feature,RangeTrack-method feature<-,RangeTrack,character-method genome,RangeTrack-method genome<-,RangeTrack-method initialize,RangeTrack-method length,RangeTrack-method max,RangeTrack-method min,RangeTrack-method position,RangeTrack-method range,RangeTrack-method ranges,RangeTrack-method RangeTrack-class seqinfo,RangeTrack-method seqlevels,RangeTrack-method seqnames,RangeTrack-method split,RangeTrack,ANY-method start,RangeTrack-method start<-,RangeTrack-method strand,RangeTrack-method strand<-,RangeTrack,ANY-method subset,RangeTrack-method values,RangeTrack-method width,RangeTrack-method width<-,RangeTrack-method [,RangeTrack,ANY,ANY,ANY-method |
| SequenceTrack class and methods | chromosome,SequenceTrack-method chromosome<-,SequenceTrack-method consolidateTrack,SequenceTrack-method drawGD,SequenceTrack-method end,SequenceTrack-method genome,SequenceTrack-method initialize,ReferenceSequenceTrack-method initialize,SequenceBSgenomeTrack-method initialize,SequenceDNAStringSetTrack-method initialize,SequenceRNAStringSetTrack-method initialize,SequenceTrack-method length,SequenceTrack-method ReferenceSequenceTrack-class RNASequenceTrack seqlevels,SequenceBSgenomeTrack-method seqlevels,SequenceTrack-method seqnames,SequenceBSgenomeTrack-method seqnames,SequenceTrack-method SequenceBSgenomeTrack-class SequenceDNAStringSetTrack-class SequenceRNAStringSetTrack-class SequenceTrack SequenceTrack-class show,ReferenceSequenceTrack-method show,SequenceBSgenomeTrack-method show,SequenceDNAStringSetTrack-method show,SequenceRNAStringSetTrack-method start,SequenceTrack-method width,SequenceTrack-method |
| Setting display parameters to control the look and feel of the plots | addScheme getScheme settings |
| StackedTrack class and methods | consolidateTrack,StackedTrack-method drawGD,StackedTrack-method initialize,StackedTrack-method setStacks,StackedTrack-method StackedTrack-class stacking,StackedTrack-method stacking<-,StackedTrack,character-method stacks,StackedTrack-method subset,StackedTrack-method [,StackedTrack,ANY,ANY,ANY-method |
| Meta-constructor for Gviz tracks fetched directly from the various UCSC data sources. | clearSessionCache UcscTrack |
