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ggbio (version 1.20.1)

Visualization tools for genomic data.

Description

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.

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Version

Version

1.20.1

License

Artistic-2.0

Last Published

February 15th, 2017

Functions in ggbio (1.20.1)

stat_gene

Calculate gene structure
theme

theme in ggbio
geom_arch

Arch geoms for GRanges object
arrangeGrobByParsingLegend

Arrange grobs by parse their legend.
plotStackedOverview

Plot stacked overview
zoom

Simple navigation for ggbio object.
GGbio

class ggbio
stat_coverage

Calculate coverage
stat_reduce

Reduce an object.
stat_mismatch

Calculate mismatch summary
ggsave

Save a ggplot object or tracks with sensible defaults
geom_alignment

Alignment geoms for GRanges object
stat_slice

Slice Rle/RleList to view them as bar or heatmap.
stat_aggregate

Generates summaries on the specified windows
geom_arrowrect

Arrowrect geoms for GRanges object
Grob-class

Grob getter
layout_karyogram

Create a karyogram layout
Plot

Plot class
plotFragLength

Plot estimated fragment length for paired-end RNA-seq data
geom_bar

Segment geoms for GRanges object
Ideogram

Plot single chromosome with cytoband
geom_chevron

Chevron geoms for GRanges object
scale_x_sequnit

scale x by unit
stat_stepping

Calculate stepping levels
geom_arrow

Arrow geoms for GRanges object
geom_segment

Segment geoms for GRanges object
autoplot

Generic autoplot function
layout_circle

Create a circle layout
scale_fill_fold_change

scale color for fold change values
stat_table

Tabulate a GRanges object
plotGrandLinear

Manhattan for GWAS
stat_identity

Transform the data to a data.frame and for multiple geoms.
geom_rect

Rect geoms for GRanges object
stat_bin

Binning method
plotSpliceSum

Plot Splice Summary from RNA-seq data
Tracked

Tracked class
ggplot

ggplot methods
scale_fill_giemsa

scale filled color to customized giemsa color.
plotRangesLinkedToData

Plot Ranges Linked with Data
rescale

rescale ggplot object
tracks

Tracks for genomic graphics