Package: ggtree 4.3.0

Guangchuang Yu

ggtree: an R package for visualization of tree and annotation data

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

Authors:Guangchuang Yu [aut, cre, cph], Tommy Tsan-Yuk Lam [aut, ths], Shuangbin Xu [aut], Lin Li [ctb], Bradley Jones [ctb], Justin Silverman [ctb], Watal M. Iwasaki [ctb], Yonghe Xia [ctb], Ruizhu Huang [ctb]

ggtree_4.3.0.tar.gz
ggtree_4.3.0.zip(r-4.7)ggtree_4.3.0.zip(r-4.6)ggtree_4.3.0.zip(r-4.5)
ggtree_4.3.0.tgz(r-4.6-any)ggtree_4.3.0.tgz(r-4.5-any)
ggtree_4.3.0.tar.gz(r-4.7-any)ggtree_4.3.0.tar.gz(r-4.6-any)
ggtree_4.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ggtree/json (API)
NEWS

# Install 'ggtree' in R:
install.packages('ggtree', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yulab-smu/ggtree/issues

On BioConductor:ggtree-4.3.0(bioc 3.24)ggtree-4.2.0(bioc 3.23)

alignmentannotationclusteringdataimportmultiplesequencealignmentphylogeneticsreproducibleresearchsoftwarevisualizationannotationsggplot2phylogenetic-trees

17.32 score 927 stars 110 packages 7.4k scripts 46k downloads 474 mentions 137 exports 71 dependencies

Last updated from:adec830cf0. Checks:1 ERROR, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR182
linux-devel-x86_64OK214
source / vignettesOK253
linux-release-x86_64OK217
macos-release-arm64OK122
macos-oldrel-arm64OK164
windows-develOK471
windows-releaseOK163
windows-oldrelOK451
wasm-releaseOK136

Exports:%+>%%<%%<+%%>%add_colorbaraesarrowas_tanglegramas_tanglegram.cophyloas_tanglegram.defaultas_tanglegram.tanglegramas.polytomycollapseDate2decimaldecimal2Dateexpandfacet_datafacet_labellerfacet_plotfacet_widthsflipfortifygeom_alinegeom_balancegeom_cladelabgeom_cladelabelgeom_cladelabel2geom_facetgeom_highlightgeom_hilightgeom_insetgeom_labelgeom_label2geom_label2_interactivegeom_motifgeom_nodelabgeom_nodelab2geom_nodepointgeom_pointgeom_point2geom_point2_interactivegeom_rangegeom_rootedgegeom_rootpointgeom_segment2geom_segment2_interactivegeom_stripgeom_striplabgeom_tanglelinkgeom_taxalinkgeom_textgeom_text2geom_text2_interactivegeom_tiplabgeom_tiplab2geom_tippointgeom_treegeom_tree2geom_treescalegeom_zoom_cladeGeomHilightEncircleGeomInteractiveCurvelinkGeomInteractiveHilightEncircleGeomInteractiveHilightRectGeomInteractiveLabelGGtreeGeomInteractivePointGGtreeGeomInteractiveSegmentGGtreeGeomInteractiveTextGGtreeget_clade_positionget_heatmap_column_positionget_taxa_nameget.pathggdensitreeggdoubletreeggexpandggplotggsaveggtreeggtree_set_interactiveggtree_unset_interactivegheatmapgroupCladegroupOTUguide_legendgzoomhexpandidentifyinsetlabel_padlayout_circularlayout_dendrogramlayout_fanlayout_inward_circularlayout_rectangularmarginMRCAmsaplotmultiplotnodebarnodeidnodelabnodepieopen_treeplot_listrange_formatread.treerevtsrotaterotate_treertreescale_colorscale_color_manualscale_color_subtreescale_colour_manualscale_colour_subtreescale_fill_manualscale_x_continuousscale_x_ggtreescale_x_rangescaleCladeset_hilight_legendStatBalancetd_filtertd_mutatetd_unnestthemetheme_dendrogramtheme_insettheme_treetheme_tree2unitvexpandviewCladexlimxlim_expandxlim_treezoomClade

Dependencies:apeaplotbase64encbslibcachemclicpp11digestdplyrevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggfunggiraphggplot2ggplotifygluegridGraphicsgtablehighrhtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrMASSmemoisemimenlmepatchworkpillarpkgconfigpurrrR6rappdirsRColorBrewerRcpprlangrmarkdownS7sassscalesstringistringrsystemfontstibbletidyrtidyselecttidytreetinytextreeioutf8vctrsviridisLitewithrxfunyamlyulab.utils

ggtree: tree visualization and annotation

Guangchuang Yu School of Basic Medical Sciences, Southern Medical University

Rendered fromggtree.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2020-09-14
Started: 2015-01-14

Readme and manuals

Help Manual

Help pageTopics
%+>%%+>%
%<%%<%
add_colorbaradd_colorbar
applyLayoutDaylightapplyLayoutDaylight
Coerce paired-tree inputs to a tanglegramas_tanglegram as_tanglegram.cophylo as_tanglegram.default as_tanglegram.tanglegram
as.polytomyas.polytomy
collapse-ggtreecollapse.ggtree
Date2decimalDate2decimal
decimal2Datedecimal2Date
expandexpand
facet_datafacet_data
facet_labellerfacet_labeller
facet_plotfacet_plot geom_facet
facet_widthsfacet_widths
flipflip
geom_alinegeom_aline
geom_balancegeom_balance
geom_cladelabgeom_cladelab
geom_cladelabelgeom_cladelabel
geom_cladelabel2geom_cladelabel2
geom_hilightgeom_highlight geom_hilight
geom_insetgeom_inset inset
geom_label2geom_label2
Create interactive label of ggtreegeom_label2_interactive
geom_motifgeom_motif
geom_nodelabgeom_nodelab
geom_nodelab2geom_nodelab2
geom_nodepointgeom_nodepoint
geom_point2geom_point2
Create interactive point of ggtreegeom_point2_interactive
geom_rangegeom_range
geom_rootedgegeom_rootedge
geom_rootpointgeom_rootpoint
geom_segment2geom_segment2
Create interactive line segments of ggtreegeom_segment2_interactive
geom_stripgeom_strip
geom_striplabgeom_striplab
Link matching taxa across a paired tree viewgeom_tanglelink
link between taxageom_taxalink
geom_text2geom_text2
Create interactive text of ggtreegeom_text2_interactive
geom_tiplabgeom_tiplab
geom_tiplab2geom_tiplab2
geom_tippointgeom_tippoint
geom_treegeom_tree
geom_tree2geom_tree2
geom_treescalegeom_treescale
geom_zoom_cladegeom_zoom_clade
ggproto classes of ggtreeGeomHilightEncircle
ggproto classes for ggiraphGeomInteractiveCurvelink
ggproto classes for ggiraphGeomInteractiveHilightEncircle
ggproto classes for ggiraphGeomInteractiveHilightRect
ggproto classes for ggiraphGeomInteractiveLabelGGtree
ggproto classes for ggiraphGeomInteractivePointGGtree
ggproto classes for ggiraphGeomInteractiveSegmentGGtree
ggproto classes for ggiraphGeomInteractiveTextGGtree
get_clade_positionget_clade_position
get_heatmap_column_positionget_heatmap_column_position
get_taxa_nameget_taxa_name
get.pathget.path
getNodeAngle.dfgetNodeAngle.df
getNodesBreadthFirst.dfgetNodesBreadthFirst.df
getSubtreegetSubtree
getSubtree.dfgetSubtree.df
getSubtreeUnrootedgetSubtreeUnrooted
getSubtreeUnrootedgetSubtreeUnrooted.df
getTreeArcAnglesgetTreeArcAngles
ggdensitreeggdensitree
Create a paired tree comparison plotggdoubletree
ggtreeggtree
Set ggtree interactive modeggtree_set_interactive
Unset ggtree interactive modeggtree_unset_interactive
gheatmapgheatmap
gzoom methodgzoom gzoom,ggtree-method gzoom,phylo-method gzoom,treedata-method
gzoomgzoom.phylo
hexpandggexpand hexpand vexpand
Padding taxa labelslabel_pad
layout_rectangularlayout_circular layout_dendrogram layout_fan layout_inward_circular layout_rectangular
Equal daylight layout method for unrooted trees.layoutDaylight
layoutEqualAnglelayoutEqualAngle
TreeAndLeaf-inspired unrooted layout.layoutTreeAndLeaf
msaplotmsaplot
multiplotmultiplot
nodebarnodebar
nodepienodepie
open_treeopen_tree
range_formatrange_format
revtsrevts
rotaterotate
rotate_treerotate_tree
rotateTreePoints.data.framerotateTreePoints.df
scale_color methodscale_color scale_color,phylo-method scale_color,treedata-method
scale_color_subtreescale_color_subtree scale_colour_subtree
scale_x_ggtreescale_x_ggtree
scale_x_rangescale_x_range
scaleCladescaleClade
set_hilight_legendset_hilight_legend
StatBalanceStatBalance
theme_dendrogramtheme_dendrogram
theme_insettheme_inset
theme_treetheme_tree
theme_tree2theme_tree2
viewCladeviewClade
xlim_expandxlim_expand
xlim_treexlim_tree
zoomCladezoomClade