Package: ggtree 3.15.0

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]

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ggtree.pdf |ggtree.html✨
ggtree/json (API)
NEWS

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

Peer review:

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

On BioConductor:ggtree-3.13.2(bioc 3.20)ggtree-3.12.0(bioc 3.19)

alignmentannotationclusteringdataimportmultiplesequencealignmentphylogeneticsreproducibleresearchsoftwarevisualizationannotationsggplot2phylogenetic-trees

16.90 score 839 stars 108 packages 5.0k scripts 34k downloads 474 mentions 117 exports 50 dependencies

Last updated 22 days agofrom:ac91900a07. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winOKOct 30 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winOKOct 30 2024
R-4.4-macOKOct 30 2024
R-4.3-winOKOct 30 2024
R-4.3-macOKOct 30 2024

Exports:%+>%%<%%<+%%>%add_colorbaraesarrowas.polytomycollapseDate2decimaldecimal2Dateexpandfacet_datafacet_labellerfacet_plotfacet_widthsflipfortifygeom_alinegeom_balancegeom_cladelabgeom_cladelabelgeom_cladelabel2geom_facetgeom_highlightgeom_hilightgeom_insetgeom_labelgeom_label2geom_motifgeom_nodelabgeom_nodelab2geom_nodepointgeom_pointgeom_point2geom_rangegeom_rootedgegeom_rootpointgeom_segment2geom_stripgeom_striplabgeom_taxalinkgeom_textgeom_text2geom_tiplabgeom_tiplab2geom_tippointgeom_treegeom_tree2geom_treescalegeom_zoom_cladeget_clade_positionget_heatmap_column_positionget_taxa_nameget.pathggdensitreeggexpandggplotggsaveggtreegheatmapgroupCladegroupOTUguide_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:apeaplotclicolorspacecpp11digestdplyrfansifarverfsgenericsggfunggplot2ggplotifygluegridGraphicsgtableisobandjsonlitelabelinglatticelazyevallifecyclemagrittrMASSMatrixmgcvmunsellnlmepatchworkpillarpkgconfigpurrrR6RColorBrewerRcpprlangscalesstringistringrtibbletidyrtidyselecttidytreetreeioutf8vctrsviridisLitewithryulab.utils

ggtree: tree visualization and annotation

Guangchuang Yu School of Basic Medical Sciences, Southern Medical University

Rendered fromggtree.Rmdusingknitr::rmarkdownon Oct 30 2024.

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

Readme and manuals

Help Manual

Help pageTopics
%+>%%+>%
%<%%<%
add_colorbaradd_colorbar
applyLayoutDaylightapplyLayoutDaylight
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
geom_motifgeom_motif
geom_nodelabgeom_nodelab
geom_nodelab2geom_nodelab2
geom_nodepointgeom_nodepoint
geom_point2geom_point2
geom_rangegeom_range
geom_rootedgegeom_rootedge
geom_rootpointgeom_rootpoint
geom_segment2geom_segment2
geom_stripgeom_strip
geom_striplabgeom_striplab
link between taxageom_taxalink
geom_text2geom_text2
geom_tiplabgeom_tiplab
geom_tiplab2geom_tiplab2
geom_tippointgeom_tippoint
geom_treegeom_tree
geom_tree2geom_tree2
geom_treescalegeom_treescale
geom_zoom_cladegeom_zoom_clade
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
ggtreeggtree
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
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