Visualization tools for genomic data

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Documentation for package ‘ggbio’ version 1.46.0

• 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