# Visualization tools for genomic data

## Documentation for package ‘ggbio’ version 1.42.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C F G H I L M N P R S T X Z misc

## -- A --

align.plots | Tracks for genomic graphics
alignPlots | Tracks for genomic graphics
Arith | Tracks for genomic graphics
Arith-method | Tracks for genomic graphics
arrangeGrobByParsingLegend | Arrange grobs by parse their legend.
autoplot | Generic autoplot function
autoplot-method | Generic autoplot function

## -- B --

backup | Tracks for genomic graphics
backup-method | Tracks for genomic graphics
bgColor | Tracks for genomic graphics
bgColor-method | Tracks for genomic graphics
bgColor<- | Tracks for genomic graphics
bgColor<--method | Tracks for genomic graphics

## -- C --

c-method | Tracks for genomic graphics
cbind-method | Tracks for genomic graphics
circle | Create a circle layout
coerce-method | Tracks for genomic graphics

## -- F --

fixed-method | Tracks for genomic graphics
fixed<--method | Tracks for genomic graphics

## -- G --

geom_alignment | Alignment geoms for GRanges object
geom_alignment-method | Alignment geoms for GRanges object
geom_arch | Arch geoms for GRanges object
geom_arch-method | Arch geoms for GRanges object
geom_arrow | Arrow geoms for GRanges object
geom_arrow-method | Arrow geoms for GRanges object
geom_arrowrect | Arrowrect geoms for GRanges object
geom_arrowrect-method | Arrowrect geoms for GRanges object
geom_bar | Segment geoms for GRanges object
geom_bar-method | Segment geoms for GRanges object
geom_chevron | Chevron geoms for GRanges object
geom_chevron-method | Chevron geoms for GRanges object
geom_rect | Rect geoms for GRanges object
geom_rect-method | Rect geoms for GRanges object
geom_segment | Segment geoms for GRanges object
geom_segment-method | Segment geoms for GRanges object
GGbio | class ggbio
ggbio | class ggbio
GGbio-class | class ggbio
ggbio-class | class ggbio
ggbioPlot-class | Plot class
ggplot.BSgenome | ggplot methods
ggplot.character | ggplot methods
ggplot.ExpressionSet | ggplot methods
ggplot.GAlignments | ggplot methods
ggplot.matrix | ggplot methods
ggplot.RsamtoolsFile | ggplot methods
ggplot.Seqinfo | ggplot methods
ggplot.SummarizedExperiment | ggplot methods
ggplot.TxDbOREnsDb | ggplot methods
ggplot.VCF | ggplot methods
ggplot.Vector | ggplot methods
ggplotGrob-class | Grob getter
ggplotPlot-class | Plot class
ggsave | Save a ggplot object or tracks with sensible defaults
Grob | Grob getter
Grob-class | Grob getter
Grob-method | Grob getter
GrobList | Grob getter
GrobList-class | Grob getter

## -- H --

hasAxis | Tracks for genomic graphics
hasAxis-method | Tracks for genomic graphics
hasAxis<- | Tracks for genomic graphics
hasAxis<--method | Tracks for genomic graphics
height | Tracks for genomic graphics
height-method | Tracks for genomic graphics
height<- | Tracks for genomic graphics
height<--method | Tracks for genomic graphics

## -- I --

Ideogram | Plot single chromosome with cytobands
Ideogram-class | Plot single chromosome with cytobands

## -- L --

labeled | Tracks for genomic graphics
labeled-method | Tracks for genomic graphics
labeled<- | Tracks for genomic graphics
labeled<--method | Tracks for genomic graphics
latticeGrob-class | Grob getter
latticePlot-class | Plot class
layout_circle | Create a circle layout
layout_circle-method | Create a circle layout
layout_karyogram | Create a karyogram layout
layout_karyogram-method | Create a karyogram layout

## -- M --

mutable | Tracks for genomic graphics
mutable-method | Tracks for genomic graphics
mutable<- | Tracks for genomic graphics
mutable<--method | Tracks for genomic graphics

## -- N --

nextView | Simple navigation for ggbio object.

## -- P --

Plot | Plot class
Plot-class | Plot class
Plot-method | Plot class
plotFragLength | Plot estimated fragment length for paired-end RNA-seq data
plotFragLength-method | Plot estimated fragment length for paired-end RNA-seq data
plotGrandLinear | Manhattan for GWAS
plotIdeogram | Plot single chromosome with cytobands
plotKaryogram | Plot stacked overview
plotRangesLinkedToData | Plot Ranges Linked with Data
plotRangesLinkedToData-method | Plot Ranges Linked with Data
plotSpliceSum | Plot Splice Summary from RNA-seq data
plotSpliceSum-method | Plot Splice Summary from RNA-seq data
plotStackedOverview | Plot stacked overview
prevView | Simple navigation for ggbio object.
print | Tracks for genomic graphics
print-method | Tracks for genomic graphics

## -- R --

rbind-method | Tracks for genomic graphics
rescale | rescale ggplot object
rescale-method | rescale ggplot object
reset | Tracks for genomic graphics
reset-method | Tracks for genomic graphics

## -- S --

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
show | Tracks for genomic graphics
show-method | Tracks for genomic graphics
stat_aggregate | Generates summaries on the specified windows
stat_aggregate-method | Generates summaries on the specified windows
stat_bin | Binning method
stat_bin-method | Binning method
stat_coverage | Calculate coverage
stat_coverage-method | Calculate coverage
stat_gene | Calculate gene structure
stat_gene-method | Calculate gene structure
stat_identity | Transform the data to a data.frame and for multiple geoms.
stat_identity-method | Transform the data to a data.frame and for multiple geoms.
stat_mismatch | Calculate mismatch summary
stat_mismatch-method | Calculate mismatch summary
stat_reduce | Reduce an object.
stat_reduce-method | Reduce an object.
stat_slice | Slice Rle/RleList to view them as bar or heatmap.
stat_slice-method | Slice Rle/RleList to view them as bar or heatmap.
stat_stepping | Calculate stepping levels
stat_stepping-method | Calculate stepping levels
stat_table | Tabulate a GRanges object
stat_table-method | Tabulate a GRanges object
summary | Tracks for genomic graphics
summary-method | Tracks for genomic graphics

## -- T --

theme_alignment | theme in ggbio
theme_clear | theme in ggbio
theme_genome | theme in ggbio
theme_noexpand | theme in ggbio
theme_null | theme in ggbio
theme_pack_panels | theme in ggbio
theme_tracks_sunset | theme in ggbio
Tracked | Tracked class
Tracked-class | Tracked class
tracks | Tracks for genomic graphics
Tracks-class | Tracks for genomic graphics

## -- X --

xlim | Tracks for genomic graphics
xlim-method | Tracks for genomic graphics
xlim<- | Tracks for genomic graphics
xlim<--method | Tracks for genomic graphics

## -- Z --

zoom | Simple navigation for ggbio object.
zoom_in | Simple navigation for ggbio object.
zoom_out | Simple navigation for ggbio object.

## -- misc --

$-method | class ggbio
$<--method | class ggbio
+-method | Generic autoplot function
+-method | class ggbio
+-method | Plot single chromosome with cytobands
[-method | Tracks for genomic graphics