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.

AuthorTengfei Yin [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Johannes Rainer [ctb]
Date of publicationNone
MaintainerMichael Lawrence <lawrence.michael@gene.com>
LicenseArtistic-2.0
Version1.22.3
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

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

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

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