ggtree: a phylogenetic tree viewer for different types of tree annotations

系統樹を描画するためのパッケージ

> library(ggtree)

Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

Attaching package: 'ggtree'

The following object is masked from 'package:github':

    get.tree

The following object is masked from 'package:igraph':

    %>%

The following objects are masked from 'package:raster':

    flip, mask, rotate

バージョン: 1.3.4

関数名 概略
%<% %<%
%<+% %<+%
%>% pipe
. .
Date2decimal Date2decimal
NJ NJ
StatHilight StatHilight
add_colorbar add_colorbar
add_legend add_legend
aes creates a lists of unevaluated expressions
annotation_clade annotation_clade
annotation_clade2 annotation_clade2
annotation_image annotation_image
apeBoot apeBoot
apeBootstrap-class Class "apeBootstrap" This class stores ape bootstrapping analysis result
as.binary as.binary
as.data.frame.phylo as.data.frame
beast-class Class "beast" This class stores information of beast output
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
decimal2Date decimal2Date
download.phylopic download.phylopic
expand expand
flip flip
fortify.phylo fortify
geom_aline geom_aline
geom_hilight geom_hilight
geom_nodepoint geom_nodepoint
geom_point2 geom_point2
geom_rootpoint geom_rootpoint
geom_segment2 geom_segment2
geom_text text annotations
geom_text2 geom_text2
geom_tiplab geom_tiplab
geom_tippoint geom_tippoint
geom_tree geom_tree
get.fields get.fields method
get.offspring.tip get.offspring.tip
get.path get.path
get.phylopic get.phylopic
get.placements get.placements method
get.subs get.subs method
get.tipseq get.tipseq method
get.tree get.tree method
get.treeinfo get.treeinfo method
get.treetext get.treetext method
getNodeNum getNodeNum
getRoot getRoot
get_clade_position get_clade_position
get_heatmap_column_position get_heatmap_column_position
get_taxa_name get_taxa_name
ggplotGrob generate a ggplot2 plot grob
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
gplot gplot
groupClade groupClade method
groupOTU groupOTU method
groupOTU.phylo groupOTU.phylo
gzoom gzoom method
gzoom.phylo gzoom
hilight hilight
hyphy-class Class "hyphy" This class stores information of HYPHY output
jplace-class Class "jplace" This class stores information of jplace file.
mask mask
merge_tree merge_tree
msaplot msaplot
nhx-class Class "nhx" This class stores nhx tree
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'
phyPML treeAnno.pml
phylopic phylopic
plot plot method
pmlToSeq pmlToSeq
r8s-class Class "r8s" This class stores output info from r8s
raxml-class Class "raxml" This class stores RAxML bootstrapping analysis result
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.r8s read.r8s
read.raxml read.raxml
read.tree read newick tree
reroot reroot method
rm.singleton.newick rm.singleton.newick
rotate rotate
rtree generate random tree
scaleClade scaleClade
scale_color scale_color method
scale_x_ggtree scale_x_ggtree
show,raxml-method show method
subview subview
theme_transparent theme_transparent
theme_tree theme_tree
theme_tree2 theme_tree2
write.jplace write.jplace 
> library(ape)


Attaching package: 'ape'

The following object is masked from 'package:ggtree':

    rotate

The following objects are masked from 'package:igraph':

    edges, mst, ring

The following objects are masked from 'package:raster':

    rotate, zoom

geom_tree

ggplot2用の系統樹レイヤー。ggplot()にはphyloクラスのデータを渡す

> rtree(n = 10) %$% ggplot(data = .) + geom_tree()

ggtree

ggplot2風に系統樹を描画

> rtree(10) %>% ggtree(.)

theme_tree

描画用テーマ

Arguments

  • bgcolor
  • fgcolor
> rtree(10) %>% ggtree(.) + theme_tree(bgcolor = "white", fgcolor = "black")

rtee

ランダムな系統樹データを作成する

ape::rtreeもある

Arguments

  • n: 系統樹の先端となる葉の数
  • rooted: logical
  • tip.label: 葉に使用するラベル
  • br
  • ...
> rtree(n = 10, rooted = TRUE, tip.label = NULL, br = runif)


Phylogenetic tree with 10 tips and 9 internal nodes.

Tip labels:
    t8, t10, t9, t2, t6, t3, ...

Rooted; includes branch lengths.