ggbio v1.20.1

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.

Functions in ggbio

Name Description
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
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Details

VignetteBuilder knitr
URL http://tengfei.github.com/ggbio/
BugReports https://github.com/tengfei/ggbio/issues
License Artistic-2.0
LazyLoad Yes
Collate AllClasses.R AllGenerics.R Cache-class.R GGbio-class.R Grob-class.R ideogram.R Tracked-class.R Plot-class.R ggplot-method.R theme.R Tracks-class.R geom_chevron-method.R geom_alignment-method.R geom_arch-method.R geom_arrow-method.R geom_arrowrect-method.R geom_rect-method.R geom_segment-method.R geom_bar-method.R layout_circle-method.R layout_karyogram-method.R layout_linear-method.R stat_aggregate-method.R stat_coverage-method.R stat_identity-method.R stat_mismatch-method.R stat_stepping-method.R stat_gene-method.R stat_table-method.R stat_bin-method.R stat_slice-method.R stat_reduce-method.R coord_genome-method.R autoplot-method.R hack.R plotGrandLinear.R plotRangesLinkedToData.R plotFragLength-method.R plotSpliceSum-method.R rescale-method.R utils.R zzz.R
biocViews Infrastructure, Visualization

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