Visualization tools for genomic data.


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Documentation for package ‘ggbio’ version 1.12.10

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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 ggplot generic method
ggplot-method ggplot generic method
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
plotSingleChrom Plot single chromosome with cytoband
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