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
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ggtree_4.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ggtree/json (API)

# 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)

alignment annotation clustering dataimport multiplesequencealignment phylogenetics reproducibleresearch software visualization annotations ggplot2 phylogenetic-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.

Target	Result	Time
bioc-checks	ERROR	182
linux-devel-x86_64	OK	214
source / vignettes	OK	253
linux-release-x86_64	OK	217
macos-release-arm64	OK	122
macos-oldrel-arm64	OK	164
windows-devel	OK	471
windows-release	OK	163
windows-oldrel	OK	451
wasm-release	OK	136

Exports:%+>%%<%%<+%%>%add_colorbar aes arrow as_tanglegram as_tanglegram.cophylo as_tanglegram.default as_tanglegram.tanglegram as.polytomy collapse Date2decimal decimal2Date expand facet_data facet_labeller facet_plot facet_widths flip fortify geom_aline geom_balance geom_cladelab geom_cladelabel geom_cladelabel2 geom_facet geom_highlight geom_hilight geom_inset geom_label geom_label2 geom_label2_interactive geom_motif geom_nodelab geom_nodelab2 geom_nodepoint geom_point geom_point2 geom_point2_interactive geom_range geom_rootedge geom_rootpoint geom_segment2 geom_segment2_interactive geom_strip geom_striplab geom_tanglelink geom_taxalink geom_text geom_text2 geom_text2_interactive geom_tiplab geom_tiplab2 geom_tippoint geom_tree geom_tree2 geom_treescale geom_zoom_clade GeomHilightEncircle GeomInteractiveCurvelink GeomInteractiveHilightEncircle GeomInteractiveHilightRect GeomInteractiveLabelGGtree GeomInteractivePointGGtree GeomInteractiveSegmentGGtree GeomInteractiveTextGGtree get_clade_position get_heatmap_column_position get_taxa_name get.path ggdensitree ggdoubletree ggexpand ggplot ggsave ggtree ggtree_set_interactive ggtree_unset_interactive gheatmap groupClade groupOTU guide_legend gzoom hexpand identify inset label_pad layout_circular layout_dendrogram layout_fan layout_inward_circular layout_rectangular margin MRCA msaplot multiplot nodebar nodeid nodelab nodepie open_tree plot_list range_format read.tree revts rotate rotate_tree rtree scale_color scale_color_manual scale_color_subtree scale_colour_manual scale_colour_subtree scale_fill_manual scale_x_continuous scale_x_ggtree scale_x_range scaleClade set_hilight_legend StatBalance td_filter td_mutate td_unnest theme theme_dendrogram theme_inset theme_tree theme_tree2 unit vexpand viewClade xlim xlim_expand xlim_tree zoomClade

Dependencies:ape aplot base64enc bslib cachem cli cpp11 digest dplyr evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics ggfun ggiraph ggplot2 ggplotify glue gridGraphics gtable highr htmltools htmlwidgets isoband jquerylib jsonlite knitr labeling lattice lazyeval lifecycle magrittr MASS memoise mime nlme patchwork pillar pkgconfig purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S7 sass scales stringi stringr systemfonts tibble tidyr tidyselect tidytree tinytex treeio utf8 vctrs viridisLite withr xfun yaml yulab.utils

ggtree: tree visualization and annotation

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Rendered fromggtree.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
%+>%	%+>%
%<%	%<%
add_colorbar	add_colorbar
applyLayoutDaylight	applyLayoutDaylight
Coerce paired-tree inputs to a tanglegram	as_tanglegram as_tanglegram.cophylo as_tanglegram.default as_tanglegram.tanglegram
as.polytomy	as.polytomy
collapse-ggtree	collapse.ggtree
Date2decimal	Date2decimal
decimal2Date	decimal2Date
expand	expand
facet_data	facet_data
facet_labeller	facet_labeller
facet_plot	facet_plot geom_facet
facet_widths	facet_widths
flip	flip
geom_aline	geom_aline
geom_balance	geom_balance
geom_cladelab	geom_cladelab
geom_cladelabel	geom_cladelabel
geom_cladelabel2	geom_cladelabel2
geom_hilight	geom_highlight geom_hilight
geom_inset	geom_inset inset
geom_label2	geom_label2
Create interactive label of ggtree	geom_label2_interactive
geom_motif	geom_motif
geom_nodelab	geom_nodelab
geom_nodelab2	geom_nodelab2
geom_nodepoint	geom_nodepoint
geom_point2	geom_point2
Create interactive point of ggtree	geom_point2_interactive
geom_range	geom_range
geom_rootedge	geom_rootedge
geom_rootpoint	geom_rootpoint
geom_segment2	geom_segment2
Create interactive line segments of ggtree	geom_segment2_interactive
geom_strip	geom_strip
geom_striplab	geom_striplab
Link matching taxa across a paired tree view	geom_tanglelink
link between taxa	geom_taxalink
geom_text2	geom_text2
Create interactive text of ggtree	geom_text2_interactive
geom_tiplab	geom_tiplab
geom_tiplab2	geom_tiplab2
geom_tippoint	geom_tippoint
geom_tree	geom_tree
geom_tree2	geom_tree2
geom_treescale	geom_treescale
geom_zoom_clade	geom_zoom_clade
ggproto classes of ggtree	GeomHilightEncircle
ggproto classes for ggiraph	GeomInteractiveCurvelink
ggproto classes for ggiraph	GeomInteractiveHilightEncircle
ggproto classes for ggiraph	GeomInteractiveHilightRect
ggproto classes for ggiraph	GeomInteractiveLabelGGtree
ggproto classes for ggiraph	GeomInteractivePointGGtree
ggproto classes for ggiraph	GeomInteractiveSegmentGGtree
ggproto classes for ggiraph	GeomInteractiveTextGGtree
get_clade_position	get_clade_position
get_heatmap_column_position	get_heatmap_column_position
get_taxa_name	get_taxa_name
get.path	get.path
getNodeAngle.df	getNodeAngle.df
getNodesBreadthFirst.df	getNodesBreadthFirst.df
getSubtree	getSubtree
getSubtree.df	getSubtree.df
getSubtreeUnrooted	getSubtreeUnrooted
getSubtreeUnrooted	getSubtreeUnrooted.df
getTreeArcAngles	getTreeArcAngles
ggdensitree	ggdensitree
Create a paired tree comparison plot	ggdoubletree
ggtree	ggtree
Set ggtree interactive mode	ggtree_set_interactive
Unset ggtree interactive mode	ggtree_unset_interactive
gheatmap	gheatmap
gzoom method	gzoom gzoom,ggtree-method gzoom,phylo-method gzoom,treedata-method
gzoom	gzoom.phylo
hexpand	ggexpand hexpand vexpand
Padding taxa labels	label_pad
layout_rectangular	layout_circular layout_dendrogram layout_fan layout_inward_circular layout_rectangular
Equal daylight layout method for unrooted trees.	layoutDaylight
layoutEqualAngle	layoutEqualAngle
TreeAndLeaf-inspired unrooted layout.	layoutTreeAndLeaf
msaplot	msaplot
multiplot	multiplot
nodebar	nodebar
nodepie	nodepie
open_tree	open_tree
range_format	range_format
revts	revts
rotate	rotate
rotate_tree	rotate_tree
rotateTreePoints.data.frame	rotateTreePoints.df
scale_color method	scale_color scale_color,phylo-method scale_color,treedata-method
scale_color_subtree	scale_color_subtree scale_colour_subtree
scale_x_ggtree	scale_x_ggtree
scale_x_range	scale_x_range
scaleClade	scaleClade
set_hilight_legend	set_hilight_legend
StatBalance	StatBalance
theme_dendrogram	theme_dendrogram
theme_inset	theme_inset
theme_tree	theme_tree
theme_tree2	theme_tree2
viewClade	viewClade
xlim_expand	xlim_expand
xlim_tree	xlim_tree
zoomClade	zoomClade