# an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

## Documentation for package ‘ggtree’ version 1.10.0

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

## Help Pages

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

ggtree-package | visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics 'ggtree' provides functions for visualizing phylogenetic tree and its associated data in R.

## -- A --

add_colorbar | add_colorbar
annotation_image | annotation_image
apeBoot | apeBoot
applyLayoutDaylight | applyLayoutDaylight
as.binary | as.binary
as.binary.phylo | as.binary
as.data.frame.phylo | as.data.frame
as.polytomy | as.polytomy

## -- C --

collapse | collapse

## -- D --

Date2decimal | Date2decimal
decimal2Date | decimal2Date
download.phylopic | download.phylopic

## -- E --

expand | expand

## -- F --

facet_plot | facet_plot
flip | flip
fortify.phylo | fortify

## -- G --

GeomHilight | StatBalance
geom_aline | geom_aline
geom_balance | geom_balance
geom_cladelabel | geom_cladelabel
geom_cladelabel2 | geom_cladelabel2
geom_hilight | geom_hilight
geom_hilight_encircle | geom_hilight_encircle
geom_label2 | geom_label2
geom_motif | geom_motif
geom_nodepoint | geom_nodepoint
geom_point2 | geom_point2
geom_range | geom_range
geom_rootpoint | geom_rootpoint
geom_segment2 | geom_segment2
geom_strip | geom_strip
geom_taxalink | geom_taxalink
geom_text2 | geom_text2
geom_tiplab | geom_tiplab
geom_tiplab2 | geom_tiplab2
geom_tippoint | geom_tippoint
geom_tree | geom_tree
geom_tree2 | geom_tree2
geom_treescale | geom_treescale
get.offspring.tip | get.offspring.tip
get.path | get.path
get.phylopic | get.phylopic
getChild.df | getChild.df
getNodeAngle.df | getNodeAngle.df
getNodesBreadthFirst.df | getNodesBreadthFirst.df
getParent.df | getParent.df
getSubtree | getSubtree
getSubtree.df | getSubtree.df
getSubtreeUnrooted | getSubtreeUnrooted
getSubtreeUnrooted.df | getSubtreeUnrooted
getTreeArcAngles | getTreeArcAngles
get_balance_position | get_balance_position
get_clade_position | get_clade_position
get_heatmap_column_position | get_heatmap_column_position
get_taxa_name | get_taxa_name
ggtree | visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics 'ggtree' provides functions for visualizing phylogenetic tree and its associated data in R.
gheatmap | gheatmap
groupClade | groupClade method
groupClade-method | groupClade method
groupOTU | groupOTU method
groupOTU-method | groupOTU method
gzoom | gzoom method
gzoom-method | gzoom method
gzoom.phylo | gzoom

## -- I --

identify.gg | identify
inset | inset

## -- L --

layoutDaylight | Equal daylight layout method for unrooted trees.
layoutEqualAngle | layoutEqualAngle

## -- M --

MRCA | MRCA
msaplot | msaplot
multiplot | multiplot

## -- N --

NJ | NJ
nodebar | nodebar
nodeid | nodeid
nodepie | nodepie

## -- O --

open_tree | open_tree

## -- P --

package-ggtree | visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics 'ggtree' provides functions for visualizing phylogenetic tree and its associated data in R.
phylopic | phylopic
print.beastList | print

## -- R --

reroot | reroot method
reroot-method | reroot method
rescale_tree | rescale_tree
revts | revts
rm.singleton.newick | rm.singleton.newick
rotate | rotate
rotateTreePoints.df | rotateTreePoints.data.fram
rotate_tree | rotate_tree

## -- S --

scaleClade | scaleClade
scale_color | scale_color method
scale_color-method | scale_color method
scale_x_ggtree | scale_x_ggtree
set_hilight_legend | set_hilight_legend
StatBalance | StatBalance
StatHilight | StatBalance
stat_balance | stat_balance
stat_hilight | stat_hilight
subview | subview

## -- T --

theme_inset | theme_inset
theme_transparent | theme_transparent
theme_tree | theme_tree
theme_tree2 | theme_tree2

## -- V --

viewClade | viewClade

## -- X --

xlim_expand | xlim_expand
xlim_tree | xlim_tree

## -- misc --

%+>% | %+>%
%<% | %<%
%<+% | %<+%
%>% | pipe
. | .