Package: Gviz 1.49.0

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:Florian Hahne [aut], Steffen Durinck [aut], Robert Ivanek [aut, cre], Arne Mueller [aut], Steve Lianoglou [aut], Ge Tan [aut], Lance Parsons [aut], Shraddha Pai [aut], Thomas McCarthy [ctb], Felix Ernst [ctb], Mike Smith [ctb]

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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

Datasets:

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)

bioconductor-package

78 exports 4.79 score 146 dependencies 45 dependents 134 mentions

Last updated 2 months agofrom:8df05b1b2d

Exports:.chrName .DisplayPars .doCache addScheme AlignmentsTrack AnnotationTrack as.list availableDefaultMapping availableDisplayPars BiomartGeneRegionTrack chromosome chromosome<-clearSessionCache consolidateTrack coords CustomTrack DataTrack DetailsAnnotationTrack displayPars DisplayPars displayPars<-drawAxis drawGD end end<-exon exon<-exportTracks feature feature<-gene gene<-GeneRegionTrack genome genome<-GenomeAxisTrack getPar getScheme group group<-HighlightTrack identifier identifier<-IdeogramTrack imageMap imageMap<-initialize OverlayTrack plotTracks position RNASequenceTrack seqinfo seqlevels seqnames SequenceTrack setCoverage setPar setStacks show split stacking stacking<-stacks start start<-strand strand<-subset symbol symbol<-tags transcript transcript<-UcscTrack values values<-width width<-

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr png prettyunits progress ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

The Gviz User Guide

Florian Hahne, Robert Ivánek

Rendered fromGviz.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-11-16
Started: 2018-12-10

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

Package: Gviz 1.49.0

Gviz: Plotting data and annotation information along genomic coordinates

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