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

'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees with their covariates and other associated data.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ggtree")
AuthorGuangchuang Yu and Tommy Tsan-Yuk Lam
Bioconductor views Alignment Annotation Clustering DataImport MultipleSequenceAlignment ReproducibleResearch Software Visualization
Date of publicationNone
MaintainerGuangchuang Yu <guangchuangyu@gmail.com>
LicenseArtistic-2.0
Version1.6.11
https://guangchuangyu.github.io/ggtree

View on Bioconductor

Man pages

add_colorbar: add_colorbar

add-TREEDATA: %<+%

add_TREEINFO: %+>%

annotation_image: annotation_image

apeBoot: apeBoot

apeBootstrap-class: Class "apeBootstrap" This class stores ape bootstrapping...

as.binary: as.binary

as.data.frame.phylo: as.data.frame

as.polytomy: as.polytomy

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

codeml-class: Class "codeml" This class stores information of output from...

codeml_mlc-class: Class "codeml_mlc" This class stores information of mlc file...

collapse: collapse

Date2decimal: Date2decimal

decimal2Date: decimal2Date

dotFun: .

download.phylopic: download.phylopic

expand: expand

facet_plot: facet_plot

flip: flip

fortify: fortify

geom_aline: geom_aline

geom_balance: geom_balance

geom_cladelabel: geom_cladelabel

geom_hilight: geom_hilight

geom_label2: geom_text2

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_balance_position: get_balance_position

get_clade_position: get_clade_position

get.fields-methods: get.fields method

get_heatmap_column_position: get_heatmap_column_position

getNodeNum: getNodeNum

get.offspring.tip: get.offspring.tip

get.path: get.path

get.phylopic: get.phylopic

get.placements-methods: get.placements method

getRoot: getRoot

get.subs-methods: get.subs method

get_taxa_name: get_taxa_name

get.tipseq-methods: get.tipseq method

get.treeinfo-methods: get.treeinfo method

get.tree-methods: get.tree method

get.treetext-methods: get.treetext method

ggtree: visualizing phylogenetic tree and heterogenous associated...

ggtree-ggproto: StatBalance

gheatmap: gheatmap

groupClade-methods: groupClade method

groupOTU-methods: groupOTU method

groupOTU.phylo: groupOTU.phylo

gzoom-methods: gzoom method

gzoom.phylo: gzoom

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

identify: identify

inset: inset

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

mask: mask

merge_tree: merge_tree

MRCA: MRCA

msaplot: msaplot

multiplot: multiplot

nhx-class: Class "nhx" This class stores nhx tree

NJ: NJ

nodebar: nodebar

nodeid: nodeid

nodepie: nodepie

open_tree: open_tree

paml_rst-class: Class "paml_rst" This class stores information of rst file...

phangorn-class: Class "phangorn" This class stores ancestral sequences...

phylip-class: Class "phylip" This class stores phylip tree(s)

phylopic: phylopic

phyPML: treeAnno.pml

pipe: pipe

plot-methods: plot method

pmlToSeq: pmlToSeq

print.beastList: print

r8s-class: Class "r8s" This class stores output info from r8s

raxml2nwk: raxml2nwk

raxml-class: Class "raxml" This class stores RAxML bootstrapping analysis...

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.phyloT: read.phyloT

read.r8s: read.r8s

read.raxml: read.raxml

reexports: Objects exported from other packages

reroot-methods: reroot method

rescale_tree: rescale_tree

rm.singleton.newick: rm.singleton.newick

rotate: rotate

rotate_tree: rotate_tree

rtree: generate random tree

scaleClade: scaleClade

scale_color-methods: scale_color method

scale_x_ggtree: scale_x_ggtree

show-methods: show method

stat_balance: stat_balance

stat_hilight: stat_hilight

subview: subview

theme_inset: theme_inset

theme_transparent: theme_transparent

theme_tree: theme_tree

theme_tree2: theme_tree2

update-TREE: %<%

viewClade: viewClade

write.jplace: write.jplace

Functions

. Man page
\%<\% Man page
\%<+\% Man page
\%>\% Man page
\%+>\% Man page
add_colorbar Man page
annotation_image Man page
apeBoot Man page
apeBootstrap-class Man page
as.binary Man page
as.binary.phylo Man page
as.data.frame.phylo Man page
as.polytomy Man page
beast-class Man page
codeml-class Man page
codeml_mlc-class Man page
collapse Man page
Date2decimal Man page
decimal2Date Man page
download.phylopic Man page
expand Man page
facet_plot Man page
flip Man page
fortify.phylo Man page
geom_aline Man page
geom_balance Man page
geom_cladelabel Man page
geom_hilight Man page
geom_label2 Man page
geom_nodepoint Man page
geom_point2 Man page
geom_range Man page
geom_rootpoint Man page
geom_segment2 Man page
geom_strip Man page
geom_taxalink Man page
geom_text2 Man page
geom_tiplab Man page
geom_tiplab2 Man page
geom_tippoint Man page
geom_tree Man page
geom_tree2 Man page
geom_treescale Man page
get_balance_position Man page
get_clade_position Man page
get.fields Man page
get.fields,apeBootstrap-method Man page
get.fields,beast-method Man page
get.fields,codeml-method Man page
get.fields,codeml_mlc-method Man page
get.fields,hyphy-method Man page
get.fields,jplace,ANY-method Man page
get.fields,jplace-method Man page
get.fields,nhx-method Man page
get.fields,paml_rst-method Man page
get.fields,phangorn-method Man page
get.fields,r8s-method Man page
get.fields,raxml-method Man page
get_heatmap_column_position Man page
getNodeNum Man page
get.offspring.tip Man page
get.path Man page
get.phylopic Man page
get.placements Man page
get.placements,jplace,ANY-method Man page
get.placements,jplace-method Man page
getRoot Man page
get.subs Man page
get.subs,codeml-method Man page
get.subs,hyphy-method Man page
get.subs,paml_rst-method Man page
get.subs,phangorn-method Man page
get_taxa_name Man page
get.tipseq Man page
get.tipseq,codeml-method Man page
get.tipseq,paml_rst-method Man page
get.tree Man page
get.tree,apeBootstrap-method Man page
get.tree,beast Man page
get.tree,beast-method Man page
get.tree,codeml-method Man page
get.tree,codeml_mlc-method Man page
get.tree,hyphy-method Man page
get.treeinfo Man page
get.treeinfo,jplace,ANY-method Man page
get.treeinfo,jplace-method Man page
get.tree,jplace-method Man page
get.tree,nhx-method Man page
get.tree,paml_rst-method Man page
get.tree,phangorn-method Man page
get.tree,phylip-method Man page
get.tree,phylo-method Man page
get.tree,r8s-method Man page
get.tree,raxml-method Man page
get.treetext Man page
get.treetext,jplace,ANY-method Man page
get.treetext,jplace-method Man page
ggtree Man page
ggtree-package Man page
gheatmap Man page
groupClade Man page
groupClade,apeBootstrap-method Man page
groupClade,beast-method Man page
groupClade,codeml-method Man page
groupClade,codeml_mlc-method Man page
groupClade,gg-method Man page
groupClade,ggplot-method Man page
groupClade,hyphy-method Man page
groupClade,jplace-method Man page
groupClade,nhx-method Man page
groupClade,paml_rst-method Man page
groupClade,phangorn-method Man page
groupClade,phylip-method Man page
groupClade,phylo-method Man page
groupClade,r8s-method Man page
groupClade,raxml-method Man page
groupOTU Man page
groupOTU,apeBootstrap-method Man page
groupOTU,beast-method Man page
groupOTU,codeml-method Man page
groupOTU,codeml_mlc-method Man page
groupOTU,gg-method Man page
groupOTU,ggplot-method Man page
groupOTU,hyphy-method Man page
groupOTU,jplace-method Man page
groupOTU,nhx-method Man page
groupOTU,paml_rst-method Man page
groupOTU,phangorn-method Man page
groupOTU,phylip-method Man page
groupOTU.phylo Man page
groupOTU,phylo-method Man page
groupOTU,r8s-method Man page
groupOTU,raxml-method Man page
gzoom Man page
gzoom,apeBootstrap-method Man page
gzoom,beast-method Man page
gzoom,codeml-method Man page
gzoom,codeml_mlc-method Man page
gzoom,gg-method Man page
gzoom,hyphy-method Man page
gzoom,nhx-method Man page
gzoom,paml_rst-method Man page
gzoom,phangorn-method Man page
gzoom.phylo Man page
gzoom,phylo-method Man page
gzoom,r8s-method Man page
gzoom,raxml-method Man page
hyphy-class Man page
identify.gg Man page
inset Man page
jplace-class Man page
mask Man page
merge_tree Man page
MRCA Man page
msaplot Man page
multiplot Man page
nhx-class Man page
NJ Man page
nodebar Man page
nodeid Man page
nodepie Man page
open_tree Man page
package-ggtree Man page
paml_rst-class Man page
phangorn-class Man page
phylip-class Man page
phylopic Man page
phyPML Man page
plot Man page
plot,beast,ANY-method Man page
plot,codeml,ANY-method Man page
plot,codeml_mlc,ANY-method Man page
plot,hyphy,ANY-method Man page
plot,paml_rst,ANY-method Man page
plot,r8s,ANY-method Man page
plot,raxml,ANY-method Man page
pmlToSeq Man page
print.beastList Man page
r8s-class Man page
raxml2nwk Man page
raxml-class Man page
read.baseml Man page
read.beast Man page
read.codeml Man page
read.codeml_mlc Man page
read.hyphy Man page
read.jplace Man page
read.nhx Man page
read.paml_rst Man page
read.phylip Man page
read.phyloT Man page
read.r8s Man page
read.raxml Man page
read.tree Man page
reexports Man page
reroot Man page
reroot,beast-method Man page
reroot,phylo-method Man page
reroot,raxml-method Man page
rescale_tree Man page
rm.singleton.newick Man page
rotate Man page
rotate_tree Man page
rtree Man page
scaleClade Man page
scale_color Man page
scale_color,apeBootstrap-method Man page
scale_color,beast-method Man page
scale_color,codeml-method Man page
scale_color,codeml_mlc-method Man page
scale_color,hyphy-method Man page
scale_color,jplace-method Man page
scale_color,nhx-method Man page
scale_color,paml_rst-method Man page
scale_color,phangorn-method Man page
scale_color,phylo-method Man page
scale_color,r8s-method Man page
scale_color,raxml-method Man page
scale_x_ggtree Man page
set.subs<-,paml_rst-method Man page
set.subs,paml_rst-method Man page
show Man page
show,apeBootstrap-method Man page
show,beast-method Man page
show,codeml-method Man page
show,codeml_mlc-method Man page
show,hyphy-method Man page
show,jplace-method Man page
show,nhx-method Man page
show,paml_rst-method Man page
show,phangorn-method Man page
show,phylip-method Man page
show,r8s-method Man page
show,raxml-method Man page
stat_balance Man page
StatBalance Man page
stat_hilight Man page
StatHilight Man page
subview Man page
theme_inset Man page
theme_transparent Man page
theme_tree Man page
theme_tree2 Man page
viewClade Man page
write.jplace Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R R/AllGenerics.R R/Date.R R/MRCA.R R/NHX.R R/NJ.R R/RAxML.R R/ape.R R/as.polytomy.R R/beast.R R/clade-functions.R R/codeml.R R/codeml_mlc.R R/experimental_function.R R/facet_plot.R R/geom_balance.R R/geom_cladelabel.R R/geom_hilight.R R/geom_label.R R/geom_point.R R/geom_range.R R/geom_segment.R R/geom_strip.R R/geom_taxalink.R R/geom_text.R R/geom_tiplab.R R/geom_tree.R R/geom_treescale.R R/ggtree-package.R R/ggtree.R R/gheatmap.R R/hyphy.R R/inset.R R/jplace.R R/layout.R R/merge_tree.R R/method-fortify.R R/method-get-tree.R R/method-groupClade.R R/method-groupOTU.R R/method-gzoom.R R/method-identify.R R/method-print.R R/method-reroot.R R/method-scale-color.R R/method-show.R R/msaplot.R R/multiplot.R R/operator.R R/paml.R R/paml_rst.R R/phangorn.R R/phylip.R R/phyloT.R R/phylopic.R R/plot.R R/r8s.R R/raxml2nwk.R R/rescale_tree.R R/subview.R R/theme.R R/tree-utilities.R R/utilities.R R/zzz.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/as.phylo.igraph.R
inst/doc
inst/doc/advanceTreeAnnotation.R
inst/doc/advanceTreeAnnotation.Rmd
inst/doc/advanceTreeAnnotation.html
inst/doc/ggtree.R
inst/doc/ggtree.Rmd
inst/doc/ggtree.html
inst/doc/ggtreeUtilities.R
inst/doc/ggtreeUtilities.Rmd
inst/doc/ggtreeUtilities.html
inst/doc/treeAnnotation.R
inst/doc/treeAnnotation.Rmd
inst/doc/treeAnnotation.html
inst/doc/treeImport.R
inst/doc/treeImport.Rmd
inst/doc/treeImport.html
inst/doc/treeManipulation.R
inst/doc/treeManipulation.Rmd
inst/doc/treeManipulation.html
inst/doc/treeVisualization.R
inst/doc/treeVisualization.Rmd
inst/doc/treeVisualization.html
inst/examples
inst/examples/FluA_H3_AA.fas
inst/examples/Genotype.txt
inst/examples/MCC_FluA_H3.tree
inst/examples/NAG_inHA1.txt
inst/examples/mlc
inst/examples/rst
inst/examples/sites.txt
inst/extdata
inst/extdata/ADH.nhx
inst/extdata/BEAST
inst/extdata/BEAST/beast_mcc.tree
inst/extdata/HYPHY
inst/extdata/HYPHY/ancseq.nex
inst/extdata/HYPHY/labelledtree.tree
inst/extdata/PAML_Baseml
inst/extdata/PAML_Baseml/mlb
inst/extdata/PAML_Baseml/rst
inst/extdata/PAML_Codeml
inst/extdata/PAML_Codeml/mlc
inst/extdata/PAML_Codeml/rst
inst/extdata/RAxML
inst/extdata/RAxML/Dated_FluA_H3.fas
inst/extdata/RAxML/RAxML_bestTree.H3
inst/extdata/RAxML/RAxML_bipartitions.H3
inst/extdata/RAxML/RAxML_bipartitionsBranchLabels.H3
inst/extdata/RAxML/RAxML_bootstrap.H3
inst/extdata/RAxML/RAxML_info.H3
inst/extdata/pa.fas
inst/extdata/pa.nwk
inst/extdata/pa_subs.csv
inst/extdata/r8s
inst/extdata/r8s/H3.r8s
inst/extdata/r8s/H3.tree
inst/extdata/r8s/H3_r8s_output.log
inst/extdata/sample.jplace
inst/extdata/sample.nwk
inst/extdata/sample.phy
inst/extdata/twoD.tree
man
man/Date2decimal.Rd man/MRCA.Rd man/NJ.Rd man/add-TREEDATA.Rd man/add_TREEINFO.Rd man/add_colorbar.Rd man/annotation_image.Rd man/apeBoot.Rd man/apeBootstrap-class.Rd man/as.binary.Rd man/as.data.frame.phylo.Rd man/as.polytomy.Rd man/beast-class.Rd man/codeml-class.Rd man/codeml_mlc-class.Rd man/collapse.Rd man/decimal2Date.Rd man/dotFun.Rd man/download.phylopic.Rd man/expand.Rd man/facet_plot.Rd man/flip.Rd man/fortify.Rd man/geom_aline.Rd man/geom_balance.Rd man/geom_cladelabel.Rd man/geom_hilight.Rd man/geom_label2.Rd man/geom_nodepoint.Rd man/geom_point2.Rd man/geom_range.Rd man/geom_rootpoint.Rd man/geom_segment2.Rd man/geom_strip.Rd man/geom_taxalink.Rd man/geom_text2.Rd man/geom_tiplab.Rd man/geom_tiplab2.Rd man/geom_tippoint.Rd man/geom_tree.Rd man/geom_tree2.Rd man/geom_treescale.Rd man/get.fields-methods.Rd man/get.offspring.tip.Rd man/get.path.Rd man/get.phylopic.Rd man/get.placements-methods.Rd man/get.subs-methods.Rd man/get.tipseq-methods.Rd man/get.tree-methods.Rd man/get.treeinfo-methods.Rd man/get.treetext-methods.Rd man/getNodeNum.Rd man/getRoot.Rd man/get_balance_position.Rd man/get_clade_position.Rd man/get_heatmap_column_position.Rd man/get_taxa_name.Rd man/ggtree-ggproto.Rd man/ggtree.Rd man/gheatmap.Rd man/groupClade-methods.Rd man/groupOTU-methods.Rd man/groupOTU.phylo.Rd man/gzoom-methods.Rd man/gzoom.phylo.Rd man/hyphy-class.Rd man/identify.Rd man/inset.Rd man/jplace-class.Rd man/mask.Rd man/merge_tree.Rd man/msaplot.Rd man/multiplot.Rd man/nhx-class.Rd man/nodebar.Rd man/nodeid.Rd man/nodepie.Rd man/open_tree.Rd man/paml_rst-class.Rd man/phangorn-class.Rd man/phyPML.Rd man/phylip-class.Rd man/phylopic.Rd man/pipe.Rd man/plot-methods.Rd man/pmlToSeq.Rd man/print.beastList.Rd man/r8s-class.Rd man/raxml-class.Rd man/raxml2nwk.Rd man/read.baseml.Rd man/read.beast.Rd man/read.codeml.Rd man/read.codeml_mlc.Rd man/read.hyphy.Rd man/read.jplace.Rd man/read.nhx.Rd man/read.paml_rst.Rd man/read.phylip.Rd man/read.phyloT.Rd man/read.r8s.Rd man/read.raxml.Rd man/reexports.Rd man/reroot-methods.Rd man/rescale_tree.Rd man/rm.singleton.newick.Rd man/rotate.Rd man/rotate_tree.Rd man/rtree.Rd man/scaleClade.Rd man/scale_color-methods.Rd man/scale_x_ggtree.Rd man/show-methods.Rd man/stat_balance.Rd man/stat_hilight.Rd man/subview.Rd man/theme_inset.Rd man/theme_transparent.Rd man/theme_tree.Rd man/theme_tree2.Rd man/update-TREE.Rd man/viewClade.Rd man/write.jplace.Rd
tests
tests/testthat
tests/testthat.R tests/testthat/test-conversion.R tests/testthat/test-geom_balance.R tests/testthat/test-geom_cladelabel.R tests/testthat/test-group.R tests/testthat/testthat.R
vignettes
vignettes/advanceTreeAnnotation.Rmd
vignettes/figures
vignettes/figures/fan_layout.gif
vignettes/figures/ggtree_objects.png
vignettes/figures/ggtree_objects_v2.png
vignettes/figures/inset_img.png
vignettes/figures/phangorn_example.png
vignettes/figures/phylobase_example.png
vignettes/figures/phylopic1.png
vignettes/figures/phylopic2.png
vignettes/figures/rotate_clade.gif
vignettes/figures/rotate_tree.gif
vignettes/figures/subview_animation.gif
vignettes/ggtree.Rmd
vignettes/ggtree.bib
vignettes/ggtreeUtilities.Rmd
vignettes/nature.csl
vignettes/toc.css
vignettes/treeAnnotation.Rmd
vignettes/treeImport.Rmd
vignettes/treeManipulation.Rmd
vignettes/treeVisualization.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.