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.

AuthorGuangchuang Yu and Tommy Tsan-Yuk Lam
Date of publicationNone
MaintainerGuangchuang Yu <guangchuangyu@gmail.com>
LicenseArtistic-2.0
Version1.6.9
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

Files in this package

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

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