# a phylogenetic tree viewer for different types of tree annotations

## Documentation for package ‘ggtree’ version 1.2.12

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

## Help Pages

A B C D E F G H I J M N P R S T V W 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
apeBootstrap-class | Class "apeBootstrap" This class stores ape bootstrapping analysis result
as.binary | as.binary
as.binary.phylo | as.binary
as.data.frame.phylo | as.data.frame

## -- B --

beast-class | Class "beast" This class stores information of beast output

## -- C --

codeml-class | Class "codeml" This class stores information of output from codeml
codeml_mlc-class | Class "codeml_mlc" This class stores information of mlc file frm codeml output
collapse | collapse

## -- D --

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

## -- E --

expand | expand

## -- F --

flip | flip
fortify.phylo | fortify

## -- G --

geom_aline | geom_aline
geom_cladelabel | geom_cladelabel
geom_hilight | geom_hilight
geom_nodepoint | geom_nodepoint
geom_point2 | geom_point2
geom_rootpoint | geom_rootpoint
geom_segment2 | geom_segment2
geom_text2 | geom_text2
geom_tiplab | geom_tiplab
geom_tippoint | geom_tippoint
geom_tree | geom_tree
geom_tree2 | geom_tree2
geom_treescale | geom_treescale
get.fields | get.fields method
get.fields-method | get.fields method
get.fields-method | Class "jplace" This class stores information of jplace file.
get.offspring.tip | get.offspring.tip
get.path | get.path
get.phylopic | get.phylopic
get.placements | get.placements method
get.placements-method | get.placements method
get.placements-method | Class "jplace" This class stores information of jplace file.
get.subs | get.subs method
get.subs-method | get.subs method
get.tipseq | get.tipseq method
get.tipseq-method | get.tipseq method
get.tree | get.tree method
get.tree,beast | get.tree method
get.tree-method | Class "beast" This class stores information of beast output
get.tree-method | get.tree method
get.treeinfo | get.treeinfo method
get.treeinfo-method | get.treeinfo method
get.treeinfo-method | Class "jplace" This class stores information of jplace file.
get.treetext | get.treetext method
get.treetext-method | get.treetext method
get.treetext-method | Class "jplace" This class stores information of jplace file.
getNodeNum | getNodeNum
getRoot | getRoot
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
groupOTU.phylo | groupOTU.phylo
gzoom | gzoom method
gzoom-method | gzoom method
gzoom.phylo | gzoom

## -- H --

hyphy-class | Class "hyphy" This class stores information of HYPHY output

## -- I --

inset | inset

## -- J --

jplace-class | Class "jplace" This class stores information of jplace file.

## -- M --

mask | mask
merge_tree | merge_tree
MRCA | MRCA
msaplot | msaplot
multiplot | multiplot

## -- N --

nhx-class | Class "nhx" This class stores nhx tree
NJ | NJ
nodebar | nodebar
nodepie | nodepie

## -- 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.
paml_rst-class | Class "paml_rst" This class stores information of rst file from PAML output
phangorn-class | Class "phangorn" This class stores ancestral sequences inferred from 'phangorn'
phylip-class | Class "phylip" This class stores phylip tree(s)
phylopic | phylopic
phyPML | treeAnno.pml
plot | plot method
plot-method | plot method
pmlToSeq | pmlToSeq

## -- R --

r8s-class | Class "r8s" This class stores output info from r8s
raxml-class | Class "raxml" This class stores RAxML bootstrapping analysis result
raxml2nwk | raxml2nwk
read.baseml | read.baseml
read.beast | read.beast
read.codeml | read.codeml
read.codeml_mlc | read.codeml_mlc
read.hyphy | read.hyphy
read.jplace | read.jplace
read.nhx | read.nhx
read.paml_rst | read.paml_rst
read.phylip | read.phylip
read.r8s | read.r8s
read.raxml | read.raxml
read.tree | read newick tree
reroot | reroot method
reroot-method | reroot method
rescale_tree | rescale_tree
rm.singleton.newick | rm.singleton.newick
rotate | rotate
rtree | generate random tree

## -- S --

scaleClade | scaleClade
scale_color | scale_color method
scale_color-method | scale_color method
scale_x_ggtree | scale_x_ggtree
set.subs-method | Class "paml_rst" This class stores information of rst file from PAML output
set.subs<--method | Class "paml_rst" This class stores information of rst file from PAML output
show | show method
show-method | Class "jplace" This class stores information of jplace file.
show-method | show method
StatHilight | StatHilight
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

## -- W --

write.jplace | write.jplace

## -- misc --

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