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.

AuthorFlorian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou, Ge Tan <ge.tan09@imperial.ac.uk>, Lance Parsons <lparsons@princeton.edu>, Shraddha Pai <shraddha.pai@utoronto.ca>
Date of publicationNone
MaintainerFlorian Hahne <florian.hahne@novartis.com>
LicenseArtistic-2.0
Version1.18.1

View on Bioconductor

Functions

[ Man page
addScheme Man page
AlignedReadTrack Man page
[,AlignedReadTrack,ANY,ANY-method Man page
AlignedReadTrack-class Man page
[,AlignedReadTrack-method Man page
AlignmentsTrack Man page
[,AlignmentsTrack,ANY,ANY-method Man page
AlignmentsTrack-class Man page
AnnotationTrack Man page
AnnotationTrack-class Man page
as.list,DisplayPars-method Man page
as.list,InferredDisplayPars-method Man page
availableDefaultMapping Man page
availableDisplayPars Man page
axTrack Man page
BiomartGeneRegionTrack Man page
BiomartGeneRegionTrack-class Man page
biomTrack Man page
bmt Man page
bmTrack Man page
chromosome Man page
chromosome<- Man page
chromosome<-,AlignmentsTrack-method Man page
chromosome<-,GdObject-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,RangeTrack-method Man page
chromosome<-,SequenceTrack-method Man page
chromosome,SequenceTrack-method Man page
clearSessionCache Man page
coerce,AnnotationTrack,UCSCData-method Man page
coerce,DataTrack,data.frame-method Man page
coerce,DisplayPars,list-method Man page
coerce,DNAString,Rle-method Man page
coerce,GeneRegionTrack,UCSCData-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,InferredDisplayPars,list-method Man page
coerce,RangeTrack,data.frame-method Man page
coerce,TxDb,GeneRegionTrack-method Man page
collapseTrack,AnnotationTrack-method Man page
collapseTrack,DataTrack-method Man page
collapseTrack,GeneRegionTrack-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
coverage,AlignedReadTrack-method Man page
coverage,AlignmentsTrack-method Man page
cpgIslands Man page
ctrack Man page
CustomTrack Man page
CustomTrack-class Man page
cyp2b10 Man page
DataTrack Man page
[,DataTrack,ANY,ANY-method Man page
DataTrack-class Man page
[,DataTrack-method Man page
denseAnnTrack Man page
DetailsAnnotationTrack Man page
DetailsAnnotationTrack-class Man page
displayPars Man page
displayPars<- Man page
DisplayPars Man page
DisplayPars-class Man page
displayPars,DisplayPars,character-method Man page
displayPars<-,DisplayPars,list-method Man page
displayPars,DisplayPars,missing-method Man page
displayPars,GdObject,character-method Man page
displayPars<-,GdObject,list-method Man page
displayPars,GdObject,missing-method Man page
displayPars<-,HighlightTrack,list-method Man page
displayPars<-,OverlayTrack,list-method 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,GenomeAxisTrack-method Man page
end<-,IdeogramTrack-method Man page
end,IdeogramTrack-method Man page
end<-,RangeTrack-method Man page
end,RangeTrack-method Man page
end,SequenceTrack-method Man page
ensGenes Man page
exon Man page
exon<- Man page
exon<-,GeneRegionTrack,character-method Man page
exon,GeneRegionTrack-method Man page
exportTracks Man page
feature Man page
feature<- Man page
feature<-,DataTrack,character-method Man page
feature,DataTrack-method Man page
feature<-,RangeTrack,character-method Man page
feature,RangeTrack-method Man page
from Man page
gcContent Man page
GdObject Man page
GdObject-class Man page
gene Man page
gene<- Man page
geneDetails Man page
gene<-,GeneRegionTrack,character-method Man page
gene,GeneRegionTrack-method Man page
geneModels Man page
GeneRegionTrack Man page
GeneRegionTrack-class Man page
GenomeAxisTrack Man page
[,GenomeAxisTrack,ANY,ANY-method Man page
GenomeAxisTrack-class Man page
[,GenomeAxisTrack-method Man page
genome<-,GdObject-method Man page
genome<-,IdeogramTrack-method Man page
genome<-,RangeTrack-method Man page
genome,RangeTrack-method Man page
genome,SequenceTrack-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
group Man page
group<- Man page
group<-,AnnotationTrack,character-method Man page
group,AnnotationTrack-method Man page
group,GdObject-method Man page
group<-,GeneRegionTrack,character-method Man page
group,GeneRegionTrack-method Man page
grouping Man page
head,InferredDisplayPars-method Man page
HighlightTrack Man page
HighlightTrack-class Man page
identifier Man page
identifier<- Man page
identifier<-,AnnotationTrack,character-method Man page
identifier,AnnotationTrack-method Man page
identifier<-,GeneRegionTrack,character-method Man page
identifier,GeneRegionTrack-method Man page
IdeogramTrack Man page
[,IdeogramTrack,ANY,ANY-method Man page
IdeogramTrack-class Man page
[,IdeogramTrack-method Man page
ideoTrack Man page
idTrack Man page
idxTrack Man page
imageMap Man page
ImageMap-class 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<-,GdObject-method Man page
isActiveSeq,RangeTrack-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,character-method Man page
names,GdObject-method Man page
NumericTrack Man page
NumericTrack-class Man page
OverlayTrack Man page
OverlayTrack-class Man page
plotTracks Man page
position Man page
position,IdeogramTrack-method Man page
position,RangeTrack-method Man page
range Man page
range,DataTrack-method Man page
range,GenomeAxisTrack-method Man page
range,RangeTrack-method Man page
ranges<-,GenomeAxisTrack-method Man page
ranges,GenomeAxisTrack-method Man page
ranges<-,RangeTrack-method Man page
ranges,RangeTrack-method Man page
RangeTrack Man page
[,RangeTrack,ANY,ANY-method Man page
RangeTrack-class Man page
[,RangeTrack-method Man page
ReferenceTrack Man page
ReferenceTrack-class Man page
refGenes Man page
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
SequenceTrack Man page
SequenceTrack-class Man page
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
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
StackedTrack Man page
[,StackedTrack,ANY,ANY-method Man page
StackedTrack-class Man page
stacking Man page
stacking<- Man page
stacking<-,StackedTrack,character-method Man page
stacking,StackedTrack-method Man page
stacks Man page
stacks,AlignmentsTrack-method Man page
stacks,StackedTrack-method Man page
start<-,GenomeAxisTrack-method Man page
start,GenomeAxisTrack-method Man page
start<-,IdeogramTrack-method Man page
start,IdeogramTrack-method Man page
start<-,RangeTrack-method Man page
start,RangeTrack-method Man page
start,SequenceTrack-method Man page
strand<-,DataTrack,ANY-method Man page
strand<-,DataTrack-method Man page
strand,DataTrack-method Man page
strand,GenomeAxisTrack-method Man page
strand<-,RangeTrack,ANY-method Man page
strand,RangeTrack-method Man page
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
symbol Man page
symbol<- Man page
symbol<-,GeneRegionTrack,character-method Man page
symbol,GeneRegionTrack-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
to Man page
transcript Man page
transcript<- Man page
transcript<-,GeneRegionTrack,character-method Man page
transcript,GeneRegionTrack-method Man page
twoGroups Man page
UcscTrack Man page
values,AlignmentsTrack-method Man page
values<-,DataTrack-method Man page
values,DataTrack-method Man page
values,GenomeAxisTrack-method Man page
values,RangeTrack-method Man page
width,GenomeAxisTrack-method Man page
width<-,IdeogramTrack-method Man page
width,IdeogramTrack-method Man page
width<-,RangeTrack-method Man page
width,RangeTrack-method Man page
width,SequenceTrack-method Man page

Files

Gviz/DESCRIPTION
Gviz/NAMESPACE
Gviz/NEWS
Gviz/R
Gviz/R/AllClasses.R Gviz/R/AllGenerics.R Gviz/R/Gviz-methods.R Gviz/R/Gviz.R
Gviz/Rplots.pdf
Gviz/TODO
Gviz/build
Gviz/build/vignette.rds
Gviz/data
Gviz/data/alTrackGenes.rda
Gviz/data/biomTrack.rda
Gviz/data/bmTrack.rda
Gviz/data/collapseTrack.rda
Gviz/data/cpgIslands.rda
Gviz/data/cyp2b10.rda
Gviz/data/denseAnnTrack.rda
Gviz/data/dtHoriz.rda
Gviz/data/geneDetails.rda
Gviz/data/geneModels.rda
Gviz/data/idTrack.rda
Gviz/data/itrack.rda
Gviz/data/twoGroups.rda
Gviz/data/ucscItems.rda
Gviz/inst
Gviz/inst/CITATION
Gviz/inst/doc
Gviz/inst/doc/Gviz.R
Gviz/inst/doc/Gviz.Rnw
Gviz/inst/doc/Gviz.pdf
Gviz/inst/extdata
Gviz/inst/extdata/GSM461176_S2_DRSC_Untreated_1_bmm.bam
Gviz/inst/extdata/GSM461176_S2_DRSC_Untreated_1_bmm.bam.bai
Gviz/inst/extdata/GSM461179_S2_DRSC_CG8144_RNAi_1_bmm.bam
Gviz/inst/extdata/GSM461179_S2_DRSC_CG8144_RNAi_1_bmm.bam.bai
Gviz/inst/extdata/biomartVersionsLatest.txt
Gviz/inst/extdata/biomartVersionsNow.txt
Gviz/inst/extdata/gapped.bam
Gviz/inst/extdata/gapped.bam.bai
Gviz/inst/extdata/snps.bam
Gviz/inst/extdata/snps.bam.bai
Gviz/inst/extdata/test.2bit
Gviz/inst/extdata/test.bam
Gviz/inst/extdata/test.bam.bai
Gviz/inst/extdata/test.bed
Gviz/inst/extdata/test.bedGraph
Gviz/inst/extdata/test.bw
Gviz/inst/extdata/test.fa
Gviz/inst/extdata/test.fa.fai
Gviz/inst/extdata/test.gff
Gviz/inst/extdata/test.gff1
Gviz/inst/extdata/test.gff2
Gviz/inst/extdata/test.gff3
Gviz/inst/extdata/test.gtf
Gviz/inst/extdata/test.wig
Gviz/inst/lib
Gviz/inst/lib/testUCSC.pl
Gviz/inst/lib/ucscUrl.pl
Gviz/inst/scripts
Gviz/inst/scripts/documentation.R
Gviz/inst/scripts/functionality.R
Gviz/inst/scripts/loadIntoEnv.R
Gviz/inst/scripts/sourcePackage.R
Gviz/inst/scripts/testBiomartGenomeMappings.R
Gviz/inst/scripts/testing.R
Gviz/inst/scripts/updateBiomartGenomeMappings.R
Gviz/man
Gviz/man/AlignedReadTrack-class.Rd Gviz/man/AlignmentsTrack-class.Rd Gviz/man/AnnotationTrack-class.Rd Gviz/man/BiomartGeneRegionTrack-class.Rd Gviz/man/CustomTrack-class.Rd Gviz/man/DataTrack-class.Rd Gviz/man/DisplayPars-class.Rd Gviz/man/GdObject-class.Rd Gviz/man/GeneRegionTrack-class.Rd Gviz/man/GenomeAxisTrack-class.Rd Gviz/man/HighlightTrack-class.Rd Gviz/man/IdeogramTrack-class.Rd Gviz/man/ImageMap-class.Rd Gviz/man/NumericTrack-class.Rd Gviz/man/OverlayTrack-class.Rd Gviz/man/RangeTrack-class.Rd Gviz/man/ReferenceTrack-class.Rd Gviz/man/SequenceTrack-class.Rd Gviz/man/StackedTrack-class.Rd Gviz/man/UcscTrack.Rd Gviz/man/collapsing.Rd Gviz/man/datasets.Rd Gviz/man/exportTracks.Rd Gviz/man/grouping.Rd Gviz/man/plotTracks.Rd Gviz/man/settings.Rd
Gviz/vignettes
Gviz/vignettes/Gviz-refs.bib
Gviz/vignettes/Gviz.Rnw
Gviz/vignettes/ucsc1.pdf
Gviz/vignettes/ucsc2.pdf

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