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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Gviz")
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>
Bioconductor views Microarray Visualization
Date of publicationNone
MaintainerFlorian Hahne <florian.hahne@novartis.com>
LicenseArtistic-2.0
Version1.20.0

View on Bioconductor

Functions

[ Man page
addScheme Man page
AlignedReadTrack Man page
[,AlignedReadTrack,ANY,ANY,ANY-method 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,ANY-method 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,AN,ANY-method 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,ANY-method 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,ANY-method 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,ANY-method 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

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

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