# an R package for visualization of tree and annotation data

## Documentation for package ‘ggtree’ version 4.1.2

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

## Help Pages

A C D E F G H I L M N O R S T V X Z misc

## -- A --

add_colorbar | add_colorbar
applyLayoutDaylight | applyLayoutDaylight
as.polytomy | as.polytomy
as_tanglegram | Coerce paired-tree inputs to a tanglegram
as_tanglegram.cophylo | Coerce paired-tree inputs to a tanglegram
as_tanglegram.default | Coerce paired-tree inputs to a tanglegram
as_tanglegram.tanglegram | Coerce paired-tree inputs to a tanglegram

## -- C --

collapse.ggtree | collapse-ggtree

## -- D --

Date2decimal | Date2decimal
decimal2Date | decimal2Date

## -- E --

expand | expand

## -- F --

facet_data | facet_data
facet_labeller | facet_labeller
facet_plot | facet_plot
facet_widths | facet_widths
flip | flip

## -- G --

GeomHilightEncircle | ggproto classes of ggtree
GeomInteractiveCurvelink | ggproto classes for ggiraph
GeomInteractiveHilightEncircle | ggproto classes for ggiraph
GeomInteractiveHilightRect | ggproto classes for ggiraph
GeomInteractiveLabelGGtree | ggproto classes for ggiraph
GeomInteractivePointGGtree | ggproto classes for ggiraph
GeomInteractiveSegmentGGtree | ggproto classes for ggiraph
GeomInteractiveTextGGtree | ggproto classes for ggiraph
geom_aline | geom_aline
geom_balance | geom_balance
geom_cladelab | geom_cladelab
geom_cladelabel | geom_cladelabel
geom_cladelabel2 | geom_cladelabel2
geom_facet | facet_plot
geom_highlight | geom_hilight
geom_hilight | geom_hilight
geom_inset | geom_inset
geom_label2 | geom_label2
geom_label2_interactive | Create interactive label of ggtree
geom_motif | geom_motif
geom_nodelab | geom_nodelab
geom_nodelab2 | geom_nodelab2
geom_nodepoint | geom_nodepoint
geom_point2 | geom_point2
geom_point2_interactive | Create interactive point of ggtree
geom_range | geom_range
geom_rootedge | geom_rootedge
geom_rootpoint | geom_rootpoint
geom_segment2 | geom_segment2
geom_segment2_interactive | Create interactive line segments of ggtree
geom_strip | geom_strip
geom_striplab | geom_striplab
geom_tanglelink | Link matching taxa across a paired tree view
geom_taxalink | link between taxa
geom_text2 | geom_text2
geom_text2_interactive | Create interactive text of ggtree
geom_tiplab | geom_tiplab
geom_tiplab2 | geom_tiplab2
geom_tippoint | geom_tippoint
geom_tree | geom_tree
geom_tree2 | geom_tree2
geom_treescale | geom_treescale
geom_zoom_clade | geom_zoom_clade
get.path | get.path
getNodeAngle.df | getNodeAngle.df
getNodesBreadthFirst.df | getNodesBreadthFirst.df
getSubtree | getSubtree
getSubtree.df | getSubtree.df
getSubtreeUnrooted | getSubtreeUnrooted
getSubtreeUnrooted.df | getSubtreeUnrooted
getTreeArcAngles | getTreeArcAngles
get_clade_position | get_clade_position
get_heatmap_column_position | get_heatmap_column_position
get_taxa_name | get_taxa_name
ggdensitree | ggdensitree
ggdoubletree | Create a paired tree comparison plot
ggexpand | hexpand
ggtree | ggtree
ggtree_set_interactive | Set ggtree interactive mode
ggtree_unset_interactive | Unset ggtree interactive mode
gheatmap | gheatmap
gzoom | gzoom method
gzoom-method | gzoom method
gzoom.phylo | gzoom

## -- H --

hexpand | hexpand

## -- I --

inset | geom_inset

## -- L --

label_pad | Padding taxa labels
layoutDaylight | Equal daylight layout method for unrooted trees.
layoutEqualAngle | layoutEqualAngle
layoutTreeAndLeaf | TreeAndLeaf-inspired unrooted layout.
layout_circular | layout_rectangular
layout_dendrogram | layout_rectangular
layout_fan | layout_rectangular
layout_inward_circular | layout_rectangular
layout_rectangular | layout_rectangular

## -- M --

msaplot | msaplot
multiplot | multiplot

## -- N --

nodebar | nodebar
nodepie | nodepie

## -- O --

open_tree | open_tree

## -- R --

range_format | range_format
revts | revts
rotate | rotate
rotateTreePoints.df | rotateTreePoints.data.frame
rotate_tree | rotate_tree

## -- S --

scaleClade | scaleClade
scale_color | scale_color method
scale_color-method | scale_color method
scale_color_subtree | scale_color_subtree
scale_colour_subtree | scale_color_subtree
scale_x_ggtree | scale_x_ggtree
scale_x_range | scale_x_range
set_hilight_legend | set_hilight_legend
StatBalance | StatBalance

## -- T --

theme_dendrogram | theme_dendrogram
theme_inset | theme_inset
theme_tree | theme_tree
theme_tree2 | theme_tree2

## -- V --

vexpand | hexpand
viewClade | viewClade

## -- X --

xlim_expand | xlim_expand
xlim_tree | xlim_tree

## -- Z --

zoomClade | zoomClade

## -- misc --

%+>% | %+>%
%<% | %<%