ggbio: Visualization tools for genomic data

The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ggbio")
AuthorTengfei Yin [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Johannes Rainer [ctb]
Bioconductor views Infrastructure Visualization
Date of publicationNone
MaintainerMichael Lawrence <lawrence.michael@gene.com>
LicenseArtistic-2.0
Version1.24.0
http://tengfei.github.com/ggbio/

View on Bioconductor

Man pages

arrangeGrobByParsingLegend: Arrange grobs by parse their legend.

autoplot-method: Generic autoplot function

geom_alignment-method: Alignment geoms for GRanges object

geom_arch-method: Arch geoms for GRanges object

geom_arrow-method: Arrow geoms for GRanges object

geom_arrowrect-method: Arrowrect geoms for GRanges object

geom_bar-method: Segment geoms for GRanges object

geom_chevron-method: Chevron geoms for GRanges object

geom_rect-method: Rect geoms for GRanges object

geom_segment-method: Segment geoms for GRanges object

ggbio-class: class ggbio

ggplot-method: ggplot methods

ggsave: Save a ggplot object or tracks with sensible defaults

Grob-class: Grob getter

layout_circle-method: Create a circle layout

layout_karyogram-method: Create a karyogram layout

nav: Simple navigation for ggbio object.

Plot-class: Plot class

plotFragLength: Plot estimated fragment length for paired-end RNA-seq data

plotGrandLinear: Manhattan for GWAS

plotRangesLinkedToData: Plot Ranges Linked with Data

plotSingleChrom: Plot single chromosome with cytoband

plotSpliceSum: Plot Splice Summary from RNA-seq data

plotStackedOverview: Plot stacked overview

rescale-method: rescale ggplot object

scale_fill_fold_change: scale color for fold change values

scale_fill_giemsa: scale filled color to customized giemsa color.

scale_x_sequnit: scale x by unit

stat_aggregate-method: Generates summaries on the specified windows

stat_bin-method: Binning method

stat_coverage-method: Calculate coverage

stat_gene-method: Calculate gene structure

stat_identity-method: Transform the data to a data.frame and for multiple geoms.

stat_mismatch-method: Calculate mismatch summary

stat_reduce-method: Reduce an object.

stat_slice-method: Slice Rle/RleList to view them as bar or heatmap.

stat_stepping-method: Calculate stepping levels

stat_table-method: Tabulate a GRanges object

theme: theme in ggbio

Tracked-class: Tracked class

tracks: Tracks for genomic graphics

Functions

align.plots Man page
alignPlots Man page
Arith Man page
Arith,Tracks,ANY-method Man page
arrangeGrobByParsingLegend Man page
autoplot Man page
autoplot,BamFileList-method Man page
autoplot,BamFile-method Man page
autoplot,BSgenome-method Man page
autoplot,character-method Man page
autoplot,ExpressionSet-method Man page
autoplot,GAlignments-method Man page
autoplot,GRangesList-method Man page
autoplot,GRanges-method Man page
autoplot,IRanges-method Man page
autoplot,matrix-method Man page
autoplot,OrganismDb-method Man page
autoplot,RangedSummarizedExperiment-method Man page
autoplot,RleList-method Man page
autoplot,Rle-method Man page
autoplot,Seqinfo-method Man page
autoplot,TabixFile-method Man page
autoplot,TxDbOREnsDb-method Man page
autoplot,VCF-method Man page
autoplot,Views-method Man page
autoplot,VRanges-method Man page
backup Man page
backup,Tracks-method Man page
bgColor Man page
bgColor<- Man page
bgColor<-,GGbio,character-method Man page
bgColor,GGbio-method Man page
bgColor<-,gg,character-method Man page
bgColor,gg-method Man page
bgColor<-,gtable,character-method Man page
bgColor,gtable-method Man page
bgColor<-,Tracked,character-method Man page
bgColor,Tracked-method Man page
+,Bioplot,Any-method Man page
cbind,Tracks-method Man page
circle Man page
coerce,Tracks,grob-method Man page
c,PlotList-method Man page
c,Tracks-method Man page
fixed<-,GGbio,logical-method Man page
fixed,GGbio-method Man page
fixed<-,gg,logical-method Man page
fixed,gg-method Man page
fixed<-,Tracked,logical-method Man page
fixed,Tracked-method Man page
geom_alignment Man page
geom_alignment,BamFile-method Man page
geom_alignment,GRangesList-method Man page
geom_alignment,GRanges-method Man page
geom_alignment,missing-method Man page
geom_alignment,OrganismDb-method Man page
geom_alignment,TxDbOREnsDb-method Man page
geom_alignment,uneval-method Man page
geom_arch Man page
geom_arch,data.frame-method Man page
geom_arch,GRanges-method Man page
geom_arch,missing-method Man page
geom_arch,uneval-method Man page
geom_arrow Man page
geom_arrow,GRanges-method Man page
geom_arrow,missing-method Man page
geom_arrowrect Man page
geom_arrowrect,GRanges-method Man page
geom_arrowrect,missing-method Man page
geom_arrowrect,uneval-method Man page
geom_arrow,uneval-method Man page
geom_bar Man page
geom_bar,ANY-method Man page
geom_bar,chevron-method Man page
geom_bar,GRanges-method Man page
geom_bar,missing-method Man page
geom_chevron Man page
geom_chevron,GRanges-method Man page
geom_chevron,missing-method Man page
geom_chevron,uneval-method Man page
geom_rect Man page
geom_rect,ANY-method Man page
geom_rect,GRanges-method Man page
geom_rect,missing-method Man page
geom_rect,uneval-method Man page
geom_segment Man page
geom_segment,ANY-method Man page
geom_segment,GRanges-method Man page
geom_segment,missing-method Man page
geom_segment,uneval-method Man page
ggbio Man page
GGbio Man page
+,GGbio,ANY-method Man page
ggbio-class Man page
GGbio-class Man page
$<-,GGbio-method Man page
$,GGbio-method Man page
ggbioPlot-class Man page
ggplot.BSgenome Man page
ggplot.character Man page
ggplot.ExpressionSet Man page
ggplot.GAlignments Man page
ggplotGrob-class Man page
ggplot.matrix Man page
ggplotPlot-class Man page
ggplot.RsamtoolsFile Man page
ggplot.Seqinfo Man page
ggplot.SummarizedExperiment Man page
ggplot.TxDbOREnsDb Man page
ggplot.VCF Man page
ggplot.Vector Man page
ggsave Man page
Grob Man page
Grob-class Man page
Grob,GGbio-method Man page
Grob,gg-method Man page
Grob,gtable-method Man page
Grob,lattice-method Man page
GrobList Man page
GrobList-class Man page
Grob-method Man page
Grob,trellis-method Man page
hasAxis Man page
hasAxis<- Man page
hasAxis<-,GGbio,logical-method Man page
hasAxis,GGbio-method}\alias{hasAxis,GGbio-method Man page
hasAxis<-,gg,logical-method Man page
hasAxis,gg-method Man page
hasAxis,gg-method Man page
hasAxis<-,Tracked,logical-method Man page
hasAxis,Tracked-method Man page
hasAxis,Tracked-method Man page
height Man page
height<- Man page
height,GGbio-method Man page
height<-,GGbio,numericORunit-method Man page
height,gg-method Man page
height<-,gg,numericORunit-method Man page
height,Tracked-method Man page
height<-,Tracked,numericORunit-method Man page
Ideogram Man page
+,Ideogram,ANY-method Man page
Ideogram-class Man page
labeled Man page
labeled<- Man page
labeled<-,GGbio,logical-method Man page
labeled,GGbio-method Man page
labeled<-,gg,logical-method Man page
labeled,gg-method Man page
labeled<-,gtable,logical-method Man page
labeled,gtable-method Man page
labeled,gTree-method Man page
labeled<-,Ideogram,logical-method Man page
labeled,Ideogram-method Man page
labeled,text-method Man page
labeled<-,Tracked,logical-method Man page
labeled,Tracked-method Man page
latticeGrob-class Man page
latticePlot-class Man page
layout_circle Man page
layout_circle,GRanges-method Man page
layout_circle,missing-method Man page
layout_circle,uneval-method Man page
layout_karyogram Man page
layout_karyogram,GRanges-method Man page
mutable Man page
mutable<- Man page
mutable<-,GGbio,logical-method Man page
mutable,GGbio-method Man page
mutable<-,gg,logical-method Man page
mutable,gg-method Man page
mutable<-,Tracked,logical-method Man page
mutable,Tracked-method Man page
nextView Man page
Plot Man page
Plot-class Man page
plotFragLength Man page
plotFragLength,character,GRanges-method Man page
Plot,GGbio-method Man page
Plot,gg-method Man page
plotGrandLinear Man page
plotIdeogram Man page
Plot,Ideogram-method Man page
plotKaryogram Man page
[,PlotList,numeric,missing,ANY-method Man page
plotRangesLinkedToData Man page
plotRangesLinkedToData,GenomicRangesORGRangesList-method Man page
plotRangesLinkedToData,RangedSummarizedExperiment-method Man page
plotSpliceSum Man page
plotSpliceSum,character,EnsDb-method Man page
plotSpliceSum,character,GRangesList-method Man page
plotSpliceSum,character,TxDb-method Man page
plotStackedOverview Man page
Plot,trellis-method Man page
prevView Man page
print Man page
print,Tracks-method Man page
rbind,Tracks-method Man page
rescale Man page
rescale,gg-method Man page
rescale,ggplot-method Man page
rescale,numeric-method Man page
reset Man page
reset,Tracks-method Man page
scale_fill_fold_change Man page
scale_fill_giemsa Man page
scale_x_sequnit Man page
show Man page
show,Tracks-method Man page
stat_aggregate Man page
stat_aggregate,GRanges-method Man page
stat_aggregate,missing-method Man page
stat_aggregate,uneval-method Man page
stat_bin Man page
stat_bin,ANY-method Man page
stat_bin,missing-method Man page
stat_bin,RleList-method Man page
stat_bin,Rle-method Man page
stat_bin,uneval-method Man page
stat_coverage Man page
stat_coverage,BamFile-method Man page
stat_coverage,GRangesList-method Man page
stat_coverage,GRanges-method Man page
stat_coverage,missing-method Man page
stat_coverage,uneval-method Man page
stat_gene Man page
stat_gene,TxDb-method Man page
stat_identity Man page
stat_identity,ANY-method Man page
stat_identity,GRanges-method Man page
stat_identity,missing-method Man page
stat_identity,RleList-method Man page
stat_identity,Rle-method Man page
stat_identity,uneval-method Man page
stat_mismatch Man page
stat_mismatch,BamFile-method Man page
stat_mismatch,GRanges-method Man page
stat_mismatch,missing-method Man page
stat_mismatch,uneval-method Man page
stat_reduce Man page
stat_reduce,GRanges-method Man page
stat_reduce,IRanges-method Man page
stat_reduce,missing-method Man page
stat_reduce,TxDbOREnsDb-method Man page
stat_reduce,uneval-method Man page
stat_slice Man page
stat_slice,missing-method Man page
stat_slice,RleList-method Man page
stat_slice,Rle-method Man page
stat_slice,uneval-method Man page
stat_stepping Man page
stat_stepping,GRanges-method Man page
stat_stepping,missing-method Man page
stat_stepping,uneval-method Man page
stat_table Man page
stat_table,GRangesList-method Man page
stat_table,GRanges-method Man page
stat_table,missing-method Man page
stat_table,uneval-method Man page
summary Man page
summary,Tracks-method Man page
theme_alignment Man page
theme_clear Man page
theme_genome Man page
theme_noexpand Man page
theme_null Man page
theme_pack_panels Man page
theme_tracks_sunset Man page
Tracked Man page
Tracked-class Man page
tracks Man page
Tracks-class Man page
[,Tracks,numeric,missing,ANY-method Man page
xlim Man page
xlim<- Man page
xlim,GRanges-method Man page
xlim,IRanges-method Man page
xlim,numeric-method Man page
xlim<-,Tracks,GRanges-method Man page
xlim<-,Tracks,IRanges-method Man page
xlim,Tracks-method Man page
xlim<-,Tracks,numeric-method Man page
zoom Man page
zoom_in Man page
zoom_out Man page

Files

.Rinstignore
DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R R/AllGenerics.R R/Cache-class.R R/GGbio-class.R R/Grob-class.R R/Plot-class.R R/Tracked-class.R R/Tracks-class.R R/autoplot-method.R R/coord_genome-method.R R/geom_alignment-method.R R/geom_arch-method.R R/geom_arrow-method.R R/geom_arrowrect-method.R R/geom_bar-method.R R/geom_chevron-method.R R/geom_rect-method.R R/geom_segment-method.R R/ggplot-method.R R/hack.R R/ideogram.R R/layout_circle-method.R R/layout_karyogram-method.R R/layout_linear-method.R R/plotFragLength-method.R R/plotGrandLinear.R R/plotRangesLinkedToData.R R/plotSpliceSum-method.R R/rescale-method.R R/stat_aggregate-method.R R/stat_bin-method.R R/stat_coverage-method.R R/stat_gene-method.R R/stat_identity-method.R R/stat_mismatch-method.R R/stat_reduce-method.R R/stat_slice-method.R R/stat_stepping-method.R R/stat_table-method.R R/theme.R R/utils.R R/zzz.R
TODO.org
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/ggbio.Rnw
inst/doc/ggbio.pdf
inst/example
inst/example/GGbio-class.R
man
man/Grob-class.Rd man/Plot-class.Rd man/Tracked-class.Rd man/arrangeGrobByParsingLegend.Rd man/autoplot-method.Rd man/geom_alignment-method.Rd man/geom_arch-method.Rd man/geom_arrow-method.Rd man/geom_arrowrect-method.Rd man/geom_bar-method.Rd man/geom_chevron-method.Rd man/geom_rect-method.Rd man/geom_segment-method.Rd man/ggbio-class.Rd man/ggplot-method.Rd man/ggsave.Rd man/layout_circle-method.Rd man/layout_karyogram-method.Rd man/nav.Rd man/plotFragLength.Rd man/plotGrandLinear.Rd man/plotRangesLinkedToData.Rd man/plotSingleChrom.Rd man/plotSpliceSum.Rd man/plotStackedOverview.Rd man/rescale-method.Rd man/scale_fill_fold_change.Rd man/scale_fill_giemsa.Rd man/scale_x_sequnit.Rd man/stat_aggregate-method.Rd man/stat_bin-method.Rd man/stat_coverage-method.Rd man/stat_gene-method.Rd man/stat_identity-method.Rd man/stat_mismatch-method.Rd man/stat_reduce-method.Rd man/stat_slice-method.Rd man/stat_stepping-method.Rd man/stat_table-method.Rd man/theme.Rd man/tracks.Rd
tests
tests/test-all.R
tests/testthat
tests/testthat/test_grob.R
vignettes
vignettes/Makefile
vignettes/fakevignettes
vignettes/fakevignettes/ggbio.Rnw
vignettes/figures
vignettes/figures/Manhattan-plotGrandLinear.pdf
vignettes/figures/autoplot_GappedAlignment.pdf
vignettes/figures/cir-single.pdf
vignettes/figures/circular-9-circle.pdf
vignettes/figures/circular-lower-link-track.pdf
vignettes/figures/coord_genome.pdf
vignettes/figures/coord_linear.pdf
vignettes/figures/coord_truncate_gaps.pdf
vignettes/figures/diagram.pdf
vignettes/figures/drawing.pdf
vignettes/figures/facet.pdf
vignettes/figures/facet_gr.pdf
vignettes/figures/geom_alignment.pdf
vignettes/figures/geom_arch.pdf
vignettes/figures/geom_arrow.pdf
vignettes/figures/geom_arrowrect.pdf
vignettes/figures/geom_bar.pdf
vignettes/figures/geom_chevron.pdf
vignettes/figures/geom_rect.pdf
vignettes/figures/geom_segment.pdf
vignettes/figures/geoms.pdf
vignettes/figures/grl.pdf
vignettes/figures/icon.pdf
vignettes/figures/karyogram.pdf
vignettes/figures/layout_circle.pdf
vignettes/figures/layout_default.pdf
vignettes/figures/layout_karyogram.pdf
vignettes/figures/man.pdf
vignettes/figures/rangeslinkedtodata-link4.pdf
vignettes/figures/splice.pdf
vignettes/figures/ssx3.pdf
vignettes/figures/stat_aggregate.pdf
vignettes/figures/stat_coverage.pdf
vignettes/figures/stat_coverage_icon.pdf
vignettes/figures/stat_gene.pdf
vignettes/figures/stat_identity.pdf
vignettes/figures/stat_mismatch.pdf
vignettes/figures/stat_reduce.pdf
vignettes/figures/stat_stepping.pdf
vignettes/figures/stat_table.pdf
vignettes/figures/track_layout.pdf
vignettes/figures/truncate_gaps.pdf
vignettes/figures/ucsc.png
vignettes/figures/vcf.pdf
vignettes/ggbio.Rnw
vignettes/knit.sh
vignettes/realvignettes
vignettes/realvignettes/ggbio.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.