ggbio: Visualization tools for genomic data.

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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.

Author
Tengfei Yin [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Johannes Rainer [ctb]
Date of publication
None
Maintainer
Michael Lawrence <lawrence.michael@gene.com>
License
Artistic-2.0
Version
1.22.0
URLs

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

Files in this package

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