Visualization tools for genomic data.

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Documentation for package ‘ggbio’ version 1.22.0

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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

-- 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 cytoband
Ideogram-class Plot single chromosome with cytoband

-- 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 cytoband
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 cytoband
[-method Tracks for genomic graphics