0% found this document useful (0 votes)

40 views87 pages

Visualize Phylogenetic Trees with ggtree

Uploaded by

Tatiana Pires

We take content rights seriously. If you suspect this is your content, claim it here.

Available Formats

Download as PDF, TXT or read online on Scribd

0% found this document useful (0 votes)

40 views87 pages

Visualize Phylogenetic Trees with ggtree

Uploaded by

Tatiana Pires

We take content rights seriously. If you suspect this is your content, claim it here.

Available Formats

Download as PDF, TXT or read online on Scribd

Package ‘ggtree’

January 9, 2025
Type Package
Title an R package for visualization of tree and annotation data
Version 3.14.0
Maintainer Guangchuang Yu <guangchuangyu@[Link]>
Description '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.
Depends R (>= 3.5.0)
Imports ape, aplot, dplyr, ggplot2 (> 3.3.6), grid, magrittr, methods,
purrr, rlang, ggfun (>= 0.1.7), [Link] (>= 0.1.6), tidyr,
tidytree (>= 0.4.5), treeio (>= 1.8.0), utils, scales, stats,
cli
Suggests emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr,
prettydoc, rmarkdown, testthat, tibble, glue
VignetteBuilder knitr
ByteCompile true
Encoding UTF-8
License Artistic-2.0

URL [Link]
Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/
B0B5NLZR1Z/
(book),
[Link]
(paper)

BugReports [Link]
biocViews Alignment, Annotation, Clustering, DataImport,
MultipleSequenceAlignment, Phylogenetics, ReproducibleResearch,
Software, Visualization
RoxygenNote 7.3.2
Roxygen list(markdown = TRUE)
git_url [Link]
git_branch RELEASE_3_20
git_last_commit a309078

1
2 Contents

git_last_commit_date 2024-10-29
Repository Bioconductor 3.20
Date/Publication 2025-01-09
Author Guangchuang Yu [aut, cre, cph]
(<[Link]
Tommy Tsan-Yuk Lam [aut, ths],
Shuangbin Xu [aut] (<[Link]
Lin Li [ctb],
Bradley Jones [ctb],
Justin Silverman [ctb],
Watal M. Iwasaki [ctb],
Yonghe Xia [ctb],
Ruizhu Huang [ctb]

Contents
ggtree-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
add_colorbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
applyLayoutDaylight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Date2decimal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
decimal2Date . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
expand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
facet_data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
facet_labeller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
facet_plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
facet_widths . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
flip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
geom_aline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
geom_balance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
geom_cladelab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
geom_cladelabel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
geom_cladelabel2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
geom_hilight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
geom_inset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
geom_label2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
geom_motif . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
geom_nodelab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
geom_nodelab2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
geom_nodepoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
geom_point2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
geom_range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
geom_rootedge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
geom_rootpoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
geom_segment2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
geom_strip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
geom_striplab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
geom_taxalink . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
geom_text2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
geom_tiplab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Contents 3

geom_tiplab2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
geom_tippoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
geom_tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
geom_tree2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
geom_treescale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
geom_zoom_clade . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
getSubtree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
getSubtreeUnrooted . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
getTreeArcAngles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
get_clade_position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
get_heatmap_column_position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
get_taxa_name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
ggdensitree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
ggtree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
gheatmap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
gzoom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
hexpand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
label_pad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
layoutDaylight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
layoutEqualAngle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
layout_rectangular . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
msaplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
multiplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
nodebar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
nodepie . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
open_tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
range_format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
reexports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
revts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
rotate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
rotate_tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
scaleClade . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
scale_color . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
scale_color_subtree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
scale_x_ggtree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
scale_x_range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
set_hilight_legend . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
StatBalance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
theme_dendrogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
theme_inset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
theme_tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
theme_tree2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
viewClade . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
xlim_expand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
xlim_tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
4 ggtree-package

zoomClade . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
%+>% . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
%<% . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

Index 85

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

Description

’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.

Author(s)

Maintainer: Guangchuang Yu <guangchuangyu@[Link]> (ORCID) [copyright holder]

Authors:

• Tommy Tsan-Yuk Lam <[Link]@[Link]> [thesis advisor]

• Shuangbin Xu <xshuangbin@[Link]> (ORCID)

Other contributors:

• Lin Li <williamlee2220@[Link]> [contributor]

• Bradley Jones <bjones@[Link]> [contributor]
• Justin Silverman <jsilve24@[Link]> [contributor]
• Watal M. Iwasaki <[Link]@[Link]> [contributor]
• Yonghe Xia <xiayh17@[Link]> [contributor]
• Ruizhu Huang <ruizhuRH@[Link]> [contributor]

See Also

Useful links:

• [Link]
dp/B0B5NLZR1Z/(book)
• [Link]
• Report bugs at [Link]
add_colorbar 5

add_colorbar add_colorbar

Description
add colorbar legend

Usage
add_colorbar(p, color, x = NULL, ymin = NULL, ymax = NULL, [Link] = 4)

Arguments
p tree view
color output of scale_color function
x x position
ymin ymin
ymax ymax
[Link] font size

Value
ggplot2 object

Author(s)
Guangchuang Yu

applyLayoutDaylight applyLayoutDaylight

Description
Apply the daylight alorithm to adjust the spacing between the subtrees and tips of the specified
node.

Usage
applyLayoutDaylight(df, node_id)

Arguments
df tree [Link]
node_id is id of the node from which daylight is measured to the other subtrees.

Value
list with tree [Link] with updated layout using daylight algorithm and max_change angle.
6 [Link]

[Link] [Link]

Description
collapse binary tree to polytomy by applying ’fun’ to ’feature’

Usage
[Link](tree, feature, fun)

Arguments
tree tree object, ’phylo’ object only
feature selected feature
fun function to select nodes to collapse

Value
polytomy tree

Author(s)
Guangchuang Yu

[Link] collapse-ggtree

Description
collapse a selected clade, which can later be expanded with the ’expand()’ fuction if necessary

Usage
## S3 method for class 'ggtree'
collapse(x = NULL, node, mode = "none", clade_name = NULL, ...)

Arguments
x tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be
used.
node internal node number
mode one of ’none’(default), ’max’, ’min’ and ’mixed’. ’none’ would simply collapse
the clade as ’tip’ and the rest will display a triangle, whose shape is determined
by the farest/closest tip of the collapsed clade to indicate it
clade_name set a name for the collapsed clade. If clade_name = NULL, do nothing
... additional parameters to set the color or transparency of the triangle
Date2decimal 7

Value

tree view

Author(s)

Guangchuang Yu

See Also

expand

Examples
x <- rtree(15)
p <- ggtree(x) + geom_tiplab()
p
p1 <- collapse(p, node = 17, mode = "mixed",
clade_name = "cclade", alpha = 0.8,
color = "grey", fill = "light blue")

Date2decimal Date2decimal

Description

convert Date to decimal format, eg "2014-05-05" to "2014.34"

Usage

Date2decimal(x)

Arguments

x Date

Value

numeric

Author(s)

Guangchuang Yu
8 expand

decimal2Date decimal2Date

Description
convert decimal format to Date, eg "2014.34" to "2014-05-05"

Usage
decimal2Date(x)

Arguments
x numerical number, eg 2014.34

Value
Date

Author(s)
Guangchuang Yu

expand expand

Description
expand collapsed clade

Usage
expand(tree_view = NULL, node)

Arguments
tree_view tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot object
will be used.
node internal node number to specify a clade. If NULL, using the whole tree

Value
tree view

Author(s)
Guangchuang Yu

geom_facet(mapping = NULL, data, geom, panel, ...)

Arguments
p tree view
mapping aes mapping for ’geom’
data data to plot by ’geom’, first column should be matched with tip label of tree
geom geom function to plot the data
panel panel name for plot of input data
... additional parameters for ’geom’

Details
’facet_plot()’ automatically re-arranges the input ’data’ according to the tree structure, visualizes the
’data’ on specific ’panel’ using the ’geom’ function with aesthetic ’mapping’ and other parameters,
and align the graph with the tree ’p’ side by side. ’geom_facet’ is a ’ggplot2’ layer version of
’facet_plot’

Value
ggplot object

Author(s)
Guangchuang Yu
facet_widths 11

Examples
tr <- rtree(10)
dd = [Link](id=tr$[Link], value=abs(rnorm(10)))
p <- ggtree(tr)
facet_plot(p, 'Trait', data = dd, geom=geom_point, mapping=aes(x=value))

facet_widths facet_widths

Description
set relative widths (for column only) of facet plots

Usage
facet_widths(p, widths)

Arguments
p ggplot or ggtree object
widths relative widths of facet panels

Value
ggplot object by redrawing the figure (not a modified version of input object)

Author(s)
Guangchuang Yu

flip flip

Description
exchange the position of 2 clades

Usage
flip(tree_view = NULL, node1, node2)
12 geom_aline

Arguments
tree_view tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be
used.
node1 node number of clade 1. It should share a same parent node with node2
node2 node number of clade 2. It should share a same parent node with node1

Value
ggplot object

Author(s)
Guangchuang Yu

Examples
[Link](123)
x <- rtree(15)
p <- ggtree(x) + geom_tiplab() +
geom_nodelab(aes(subset=!isTip, label=node), hjust = -.1, color = "red")
flip(p, 23, 24) ## Depends on the condition of your tree

geom_aline geom_aline

Description
add horizontal align lines layer to a tree

Usage
geom_aline(mapping = NULL, linetype = "dotted", linewidth = 1, ...)

Arguments
mapping aes mapping
linetype set line type of the line, defaults to "dotted"
linewidth set width of the line, defaults to 1
... additional parameter

Details
’geom_aline’align all tips to the longest one by adding padding characters to the right side of the
tip.

Value
aline layer

Author(s)
Yu Guangchuang
geom_balance 13

geom_balance geom_balance

Description
highlights the two direct descendant clades of an internal node

Usage
geom_balance(
node,
fill = "steelblue",
color = "white",
alpha = 0.5,
extend = 0,
extendto = NULL
)

Arguments
node selected node (balance) to highlight its two direct descendant
fill color to fill in the highlight rectangle, default to "steelblue"
color color to outline highlight rectangle and divide balance, defaults to "white"
alpha alpha (transparency) for the highlight rectangle, defaults to 0.5
extend extend xmax of the highlight rectangle by the value of extend
extendto extend xmax of the highlight rectangle to the value of extendto

Details
Particularly useful when studying neighboring clades. Note that balances that correspond to multi-
chotomies will not be displayed.

Value
ggplot2

Author(s)
Justin Silverman and modified by Guangchuang Yu

References
J. Silverman, et al. A phylogenetic transform enhances analysis of compositional microbiota data.
(in preparation)
For more detailed demonstration, please refer to chapter 5.2.2 of Data Integration, Manipulation
and Visualization of Phylogenetic Trees [Link]
by Guangchuang Yu.
14 geom_cladelab

Examples
library(ggtree)
[Link](123)
tr<- rtree(15)
x <- ggtree(tr)
x + geom_balance(17)

geom_cladelab geom_cladelab

Description
annotate a clade with bar and text label or (image)

Usage
geom_cladelab(
node = NULL,
label = NULL,
data = NULL,
mapping = NULL,
geom = "text",
parse = FALSE,
...
)

Arguments
node selected node to annotate, when data and mapping is NULL, it is required.
label character, character to be showed, when data and mapping is NULL, it is re-
quired.
data [Link], the data to be displayed in the annotation, defaults to NULL.
mapping Set of aesthetic mappings, defaults to NULL. The detail see the following ex-
planation.
geom character, one of ’text’, ’label’, ’shadowtext’, ’image’ and ’phylopic’, defaults
to ’text’, and the parameter see the Aesthetics For Specified Geom.
parse logical, whether parse label to emoji font, defaults to FALSE.
... additional parameters, see also following section.
additional parameters can refer the following parameters.
• offset distance bar and tree, offset of bar and text from the clade, defaults
to 0.
• [Link] distance bar and text, offset of text from bar, defaults to 0.
• align logical, whether align clade lab, defaults to FALSE.
• extend numeric, extend the length of bar, defaults to 0.
• angle numeric or ’auto’, if angle is auto, the angle of text will be calculated
automatically, which is useful for the circular etc layout, defaults to 0.
• horizontal logical, whether set label to horizontal, defaults to TRUE.
geom_cladelab 15

• barsize the width of line, defaults to 0.5.

• barcolour the colour of line, defaults to ’black’.
• fontsize the size of text, defaults to 3.88.
• textcolour the colour of text, defaults to ’black’.
• imagesize the size of image, defaults to 0.05.
• imagecolor the colour of image, defaults to NULL, when geom="phylopic",
it should be required.
The parameters also can be set in mapping, when data is provided. Note: the
barsize, barcolour, fontsize, textcolour, imagesize and imagecolor should not be
set in mapping (aesthetics). When the color and size are not be set in mapping,
user can modify them to adjust the attributes of specified geom.

Aesthetics For Specified Geom

geom_cladelab() understands the following aesthetics for geom="text"(required aesthetics are in
bold):
• node selected node to hight light, it is required.
• label labels to be shown, it is required.
• colour the colour of text, defaults to "black".
• size the size of text, defaults to 3.88.
• angle the angle of text, defaults to 0.
• hjust A numeric vector specifying horizontal justification, defaults to 0.
• vjust A numeric vector specifying vertical justification, defaults to 0.5.
• alpha the transparency of text, defaults to NA.
• family the family of text, defaults to ’sans’.
• fontface the font face of text, defaults to 1 (plain), others are 2 (bold), 3 (italic), 4 ([Link]).
• lineheight The height of a line as a multiple of the size of text, defaults to 1.2 .
when the colour, size are not be set in mapping, and user want to modify the colour of text, they
should use textcolour, fontsize to avoid the confusion with bar layer annotation.
geom_cladelab() understands the following aesthethics for geom="label" (required aesthetics are
in bold):
• node selected node to hight light, it is required.
• label labels to be shown, it is required.
• colour the colour of text, defaults to "black".
• fill the background colour of the label, defaults to "white".
• size the size of text, defaults to 3.88.
• angle the angle of text, defaults to 0.
• hjust A numeric vector specifying horizontal justification, defaults to 0.
• vjust A numeric vector specifying vertical justification, defaults to 0.5.
• alpha the transparency of text, defaults to NA.
• family the family of text, defaults to ’sans’.
• fontface the font face of text, defaults to 1 (plain), others are 2 (bold), 3 (italic), 4 ([Link]).
• lineheight The height of a line as a multiple of the size of text, defaults to 1.2 .
16 geom_cladelab

when the colour, size are not be set in mapping, and user want to modify the colour of text, they
should use textcolour, fontsize to avoid the confusion with bar layer annotation.
geom_cladelab() understands the following aesthethics for geom="shadowtext" (required aesthet-
ics are in bold):

• node selected node to hight light, it is required.

• label labels to be shown, it is required.
• colour the colour of text, defaults to "black".
• [Link] the background colour of text, defaults to ’black’.
• bg.r the width of background text, defaults to 0.1.
• size the size of text, defaults to 3.88.
• angle the angle of text, defaults to 0.
• hjust A numeric vector specifying horizontal justification, defaults to 0.
• vjust A numeric vector specifying vertical justification, defaults to 0.5.
• alpha the transparency of text, defaults to NA.
• family the family of text, defaults to ’sans’.
• fontface the font face of text, defaults to 1 (plain), others are 2 (bold), 3 (italic), 4 ([Link]).
• lineheight The height of a line as a multiple of the size of text, defaults to 1.2 .

• node selected node to hight light, it is required.

• label labels to be shown, it is required.
• image the image to be annotated, when geom="phylopic", the uid of phylopic databases, it is
required.
• colour the color of image, defaults to NULL.
• size the size of image, defaults to 0.05.
• alpha the alpha of image, defaults to 0.8.

when the colour, size are not be set in mapping, and user want to modify the colour of image, they
should use imagecolour, imagesize to avoid the confusion with bar layer annotation.

Examples
[Link](2015-12-21)
tree <- rtree(30)
data <- [Link](id=c(34, 56),
annote=c("another clade", "long clade names"),
image=c("7fb9bea8-e758-4986-afb2-95a2c3bf983d",
"0174801d-15a6-4668-bfe0-4c421fbe51e8"),
group=c("A", "B"),
offset=c(0.1, 0.1),
[Link]=c(0.1, 0.2))

p <- ggtree(tree) + xlim(NA, 6)

geom_cladelabel 17

p + geom_cladelab(node=45, label="test label") +

geom_cladelab(node=34, label="another clade")
p2 <- p + geom_cladelab(data=data,
mapping=aes(
node=id,
label=annote,
image=image,
color=group,
offset=offset
),
geom="shadowtext",
hjust=0.5,
align=TRUE,
horizontal=FALSE,
angle=90,
[Link] = FALSE
)
p2

geom_cladelabel geom_cladelabel

Description
annotate a clade with bar and text label

Usage
geom_cladelabel(
node,
label,
offset = 0,
[Link] = 0,
extend = 0,
align = FALSE,
barsize = 0.5,
fontsize = 3.88,
angle = 0,
geom = "text",
hjust = 0,
color = NULL,
fill = NA,
family = "sans",
parse = FALSE,
horizontal = TRUE,
...
)

Arguments
node selected node
label clade label
18 geom_cladelabel2

offset offset of bar and text from the clade

[Link] offset of text from bar
extend extend bar height
align logical
barsize size of bar
fontsize size of text
angle angle of text
geom one of ’text’ or ’label’
hjust justify text horizontally
color color for clade & label, of length 1 or 2
fill fill label background, only work with geom=’label’
family sans by default, can be any supported font
parse logical, whether parse label
horizontal logical, whether set label to horizontal, defaults to TRUE.
... additional parameter

Value
ggplot layers

Author(s)
Guangchuang Yu

node selected node

label clade label
offset offset of bar and text from the clade
[Link] offset of text from bar
[Link] offset of bar from text
align logical
barsize size of bar
fontsize size of text
hjust justify text horizontally
geom one of ’text’ or ’label’
color color for clade & label, of length 1 or 2
family sans by default, can be any supported font
parse logical, whether parse label
horizontal logical, whether set label to horizontal, defaults to TRUE.
... additional parameter

Value

ggplot layers

Author(s)

JustGitting

See Also

geom_cladelabel
20 geom_hilight

geom_hilight geom_hilight

Description
layer of hilight clade

Usage
geom_hilight(
data = NULL,
mapping = NULL,
node = NULL,
type = "auto",
[Link] = FALSE,
...
)

geom_highlight(
data = NULL,
mapping = NULL,
node = NULL,
type = "auto",
[Link] = FALSE,
...
)

Arguments
data [Link], The data to be displayed in this layer, defaults to NULL.
mapping Set of aesthetic mappings, defaults to NULL.
node selected node to hilight, when data and mapping is NULL, it is required.
type the type of layer, defaults to auto, meaning rectangular, circular, slanted, fan,
inward_circular, radial, equal_angle, ape layout tree will use rectangular layer,
unrooted and daylight layout tree use will use encircle layer. You can specify this
parameter to rect (rectangular layer) or encircle (encircle layer), ’gradient’
(gradient color), ’roundrect’ (round rectangular layer).
[Link] logical, whether set the high light layer to the bottom in all layers of ’ggtree’
object, default is FALSE.
... additional parameters, see also the below and Aesthetics section.
• align control the align direction of the edge of high light rectangular. Op-
tions is ’none’ (default), ’left’, ’right’, ’both’. This argument only work
when the ’geom_hilight’ is plotting using geom_hilight(mapping=aes(...)).
• [Link] character, the direction of gradient color, defaults to
’rt’ meaning the locations of gradient color is from root to tip, options are
’rt’ and ’tr’.
• [Link] integer, desired length of the sequence of gradient
color, defaults to 2.
• roundrect.r numeric, the radius of the rounded corners, when roundrect=TRUE,
defaults to 0.05.
geom_hilight 21

Details
geom_hilight supports [Link] as input. And aesthetics of layer can be mapped. you can see
the Aesthetics section to set parameters.

Value
a list object.

Aesthetics
geom_hilight() understands the following aesthetics for rectangular layer (required aesthetics are
in bold):

• node selected node to hight light, it is required.

• colour the colour of margin, defaults to NA.
• fill the colour of fill, defaults to ’steelblue’.
• alpha the transparency of fill, defaults to 0.5.
• extend extend xmax of the rectangle, defaults to 0.
• extendto specify a value, meaning the rectangle extend to, defaults to NULL.
• linetype the line type of margin, defaults to 1.
• linewidth the width of line of margin, defaults to 0.5.

geom_hilight() understands the following aesthethics for encircle layer (required aesthetics are
in bold):

• node selected node to hight light, it is required.

• colour the colour of margin, defaults to ’black’.
• fill the colour of fill, defaults to ’steelblue’.
• alpha the transparency of fill, defaults to 0.5.
• expand expands the xspline clade region, defaults to 0.
• spread control the size, when only one point.
• linewidth the width of line of margin, defaults to 0.5.
• linetype the line type of margin, defaults to 1.
• s_shape the shape of the spline relative to the control points, defaults to 0.5.
• s_open whether the spline is a line or a closed shape, defaults to FALSE.

Author(s)
Guangchuang Yu and Shuangbin Xu

References
For more detailed demonstration, please refer to chapter 5.2.2 of Data Integration, Manipulation
and Visualization of Phylogenetic Trees [Link]
by Guangchuang Yu.
22 geom_inset

Examples
library(ggplot2)
[Link](102)
tree <- rtree(60)
p <- ggtree(tree)
p1 <- p + geom_hilight(node=62) + geom_hilight(node=88, fill="red")
p1
dat <- [Link](id=c(62, 88), type=c("A", "B"))
p2 <- p + geom_hilight(data=dat, mapping=aes(node=id, fill=type))
p2
p3 <- p + geom_hilight(data=dat, mapping=aes(node=id, fill=type), align="left")
p4 <- p + geom_hilight(data=dat, mapping=aes(node=id, fill=type), align="right")
p5 <- p + geom_hilight(data=dat, mapping=aes(node=id, fill=type), align="both")
# display the high light layer with gradiental color rectangular.
p6 <- p + geom_hilight(data=dat, mapping=aes(node=id, fill=type), type = "gradient", alpha=0.68)
p7 <- p + geom_hilight(data=dat, mapping=aes(node=id, fill=type),
type = "gradient", [Link]="tr", alpha=0.68)
# display the high light layer with round rectangular.
p8 <- p + geom_hilight(data=dat, mapping=aes(node=id, fill=type), type = "roundrect", alpha=0.68)
p2/ p3/ p4/ p5 / p6/ p7/ p8

geom_inset geom_inset

Description
gemo_inset can add subplots to tree by accepting a list of ggplot objects that are ancestral stats or
data associated with selected nodes in the tree. These ggplot objects can be any kind of charts or
hybrid of of these charts.
add subplots as insets in a tree

Usage
geom_inset(
insets,
width = 0.1,
height = 0.1,
hjust = 0,
vjust = 0,
x = "node",
reverse_x = FALSE,
reverse_y = FALSE
)

inset(
tree_view,
insets,
width,
height,
hjust = 0,
vjust = 0,
x = "node",
geom_label2 23

reverse_x = FALSE,
reverse_y = FALSE
)

Arguments

insets a list of ggplot objects, named by node number

width width of the inset, relative to the range of x-axis, defaults to .1
height height of the inset, relative to the range of y-axis, defaults to .1
hjust adjust the horizontal position of the charts, charts will go left if hjust > 0
vjust adjust the vertical position of the charts, charts will go down if vjust > 0
x the position where users want to place the charts, one of ’node’ (default) and
’branch’
reverse_x whether to reverse x axis of the charts by ’ggplot2::scale_x_reverse’, defaults to
’FALSE’
reverse_y whether to reverse y axis of the charts by ’ggplot2::scale_y_reverse’, defaults to
’FALSE’
tree_view tree view

Details

Users can also use

Value

inset layer
tree view with insets

Author(s)

Guangchuang Yu

References

For demonstration of this function, please refer to chapter 8.3 of Data Integration, Manipulation
and Visualization of Phylogenetic Trees [Link]
by Guangchuang Yu.

geom_label2 geom_label2

Description

geom_label2 support aes(subset) via setup_data

24 geom_label2

Usage
geom_label2(
mapping = NULL,
data = NULL,
...,
stat = "identity",
position = "identity",
family = "sans",
parse = FALSE,
nudge_x = 0,
nudge_y = 0,
[Link] = unit(0.25, "lines"),
label.r = unit(0.15, "lines"),
[Link] = 0.25,
[Link] = TRUE,
[Link] = NA,
[Link] = TRUE
)

Arguments
mapping Set of aesthetic mappings, defaults to NULL.
data A layer specific dataset - only needed if you want to override the plot defaults.
... other arguments passed on to ’layer’.
stat Name of the stat to modify data.
position The position adjustment to use for overlapping points on this layer.
family "sans" by default, can be any supported font.
parse if ’TRUE’, the labels will be parsed as expressions, defaults to ’FALSE’.
nudge_x adjust the horizontal position of the labels.
nudge_y adjust the vertical position of the labels.
[Link] Amount of padding around label, defaults to ’unit(0.25, "lines")’.
label.r Use to set the radius of rounded corners of the label, defaults to ’unit(0.15,
"lines")’.
[Link] Size of label border, in mm, defaults to 0.25.
[Link] If "FALSE" (default), missing values are removed with a warning. If "TRUE",
missing values are silently removed, logical.
[Link] Whether to show legend, logical, defaults to "NA".
[Link] Whether to inherit aesthetic mappings, logical, defaults to "TRUE".

Details
’geom_label2’ is a modified version of geom_label, with subset aesthetic supported

Value
label layer
geom_motif 25

Author(s)
Guangchuang Yu

References
For more detailed demonstration of this function, please refer to chapter A.4.5 of Data Integration,
Manipulation and Visualization of Phylogenetic Trees [Link]
[Link] by Guangchuang Yu.

add node label for circular layout

Usage

geom_nodelab2(
mapping = NULL,
nudge_x = 0,
nudge_y = 0,
geom = "text",
hjust = 0.5,
...
)

Arguments

mapping aesthetic mappings, defaults to NULL

nudge_x horizontal adjustment to nudge labels, defaults to 0
nudge_y vertical adjustment to nudge labels, defaults to 0
geom one of ’text’, "shadowtext", ’label’, ’image’ and ’phylopic’
hjust horizontal alignment, defaults to 0.5
... additional parameters, see also the additional parameters of geom_tiplab().

Value

node label layer

Author(s)

Guangchuang Yu

geom_nodepoint geom_nodepoint

Description

add node point layer to a tree

28 geom_nodepoint

Usage

geom_nodepoint(
mapping = NULL,
data = NULL,
position = "identity",
[Link] = FALSE,
[Link] = NA,
[Link] = TRUE,
...
)

Arguments

mapping Set of aesthetic mapping created by aes(). If [Link] = TRUE, the map-
ping can be inherited from the plot mapping as specified in the call to ggplot().
data The data to be displayed in this layer. If ’NULL’ (the default), the data is inher-
ited from the plot data as specified in the call to ggplot().
position Position adjustment.
[Link] logical. If ’FALSE’ (default), missing values are removed with a warning. If
’TRUE’, missing values are silently removed.
[Link] logical. Should this layer be included in the legends? ’NA’, the default, includes
if any aesthetics are mapped. ’FALSE’ never includes, and ’TRUE’ always
includes.
[Link] logical (defaults to ’TRUE’). If ’FALSE’, overrides the default aesthetics, rather
then combining with them.
... addtional parameters that passed on to this layer. These are often aesthetics,
used to set an aesthetic to a fixed value, like colour = "red" or size = 3.

Value

node point layer

Author(s)

Guangchuang Yu library(ggtree) tr<- rtree(15) x <- ggtree(tr) x + geom_nodepoint()

References

For more detailed demonstration, please refer to chapter 4.3.2 of Data Integration, Manipulation
and Visualization of Phylogenetic Trees [Link]
by Guangchuang Yu.
geom_point2 29

geom_point2 geom_point2

Description

geom_point2 is a modified version of geom_point that supports aes(subset)

Usage

geom_point2(
mapping = NULL,
data = NULL,
stat = "identity",
position = "identity",
[Link] = FALSE,
[Link] = NA,
[Link] = TRUE,
...
)

Arguments

mapping Set of aesthetic mapping created by aes(). If [Link] = TRUE, the map-
ping can be inherited from the plot mapping as specified in the call to ggplot().
data The data to be displayed in this layer. If ’NULL’ (the default), the data is inher-
ited from the plot data as specified in the call to ggplot().
stat Name of the statistical transformation to be used on the data for this layer.
position Position adjustment.
[Link] logical. If ’FALSE’ (default), missing values are removed with a warning. If
’TRUE’, missing values are silently removed.
[Link] logical. Should this layer be included in the legends? ’NA’, the default, includes
if any aesthetics are mapped. ’FALSE’ never includes, and ’TRUE’ always
includes.
[Link] logical (defaults to ’TRUE’). If ’FALSE’, overrides the default aesthetics, rather
then combining with them.
... addtional parameters that passed on to this layer. These are often aesthetics,
used to set an aesthetic to a fixed value, like colour = "red" or size = 3.

Details

geom_point2 creates scatterplots, just similar to ggplot2::geom_point. It extends the ggplot2::geom_point

to support filtering via the subset aesthetic mapping (see Aesthetics section).

Value

point layer
30 geom_point2

Aesthetics
geom_point2() understands the following aesthetics
• subset logical expression indicating elements or rows to keep: missing values are taken as
false; should be in aes().
• colour the colour of point, defaults to "black".
• fill the colour of fill, defaults to "black".
• alpha the transparency of fill, defaults to 1.
• size the size of point, defaults to 1.5.
• shape specify a shape, defaults to 19.
• stroke control point border thickness of point, defaults to 0.5.

Author(s)
Guangchuang Yu

References
1. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam (2017). ggtree: an R package for visualization
and annotation of phylogenetic trees with their covariates and other associated data. Methods
in Ecology and Evolution, 8(1):28-36. [Link]
2. G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated
data on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043.
[Link]
3. G Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformat-
ics, 2020, 69:e96. [Link]
For more information about tree visualization, please refer to the online book [Link]
top/treedata-book/

See Also
geom_point; geom_rootpoint add point of root; geom_nodepoint add points of internal nodes;
geom_tippoint add points of external nodes (also known as tips or leaves).

Examples
library(ggtree)
## add point by aes(subset)
tr <- rtree(10)
# group tip and node
ggtree(tr) + geom_point2(aes(shape=isTip, color=isTip), size=3)
# specify a node to display
ggtree(tr) + geom_point2(aes(subset=(node==15)), shape=21, size=5, fill='green')
# specify a tip to display
ggtree(tr) + geom_point2(aes(subset=(label %in% c("t1", "t3"))), shape=21, size=5, fill='green')

## color point with continuous variables

library(ggtree)
library(treeio)
library(ggplot2)
beast_file <- [Link]("examples/MCC_FluA_H3.tree", package="ggtree")
beast_tree <- [Link](beast_file)
geom_range 31

p <- ggtree(beast_tree) +
geom_tiplab(hjust = -.1)+
geom_nodepoint(aes(fill = rate), shape = 21, size = 4) +
scale_fill_continuous(low = 'blue', high = 'red') +
theme_tree2() + theme([Link] = 'right')
p

geom_range geom_range

Description

horizontal bar of range (HPD, range etc) on nodes to present uncertainty of evolutionary inference

Usage

geom_range(range, center = "auto", ...)

Arguments

range range(interval) to be displayed, e.g. "height_0.95_HPD"

center center of the range, mean, median or auto (default, the center of the range)
... additional parameter, e.g. color, linewidth, alpha

Value

ggplot layer

Author(s)

Guangchuang Yu

References

For demonstration of this function, please refer to chapter 5.2.4 of Data Integration, Manipulation
and Visualization of Phylogenetic Trees [Link]
by Guangchuang Yu.
32 geom_rootedge

geom_rootedge geom_rootedge

Description
display root edge layer for a tree

Usage
geom_rootedge(rootedge = NULL, ...)

Arguments
rootedge length of rootedge; use phylo$[Link] if rootedge = NULL (default).
... additional parameters
Additional parameters can be referred to the following parameters:
• size control the width of rootedge, defaults to 0.5.
• colour color of rootedge, defaults to black.
• linetype the type of line, defaults to 1.
• alpha modify colour transparency, defaults to 1.

Details
geom_rootedge is used to create a rootedge as ggtree doesn’t plot the root edge by default.

Value
ggtree rootedge layer

Author(s)
Guangchuang Yu

Examples
library(ggtree)
[Link](123)
## with root edge = 1
tree1 <- [Link](text='((A:1,B:2):3,C:2):1;')
ggtree(tree1) + geom_tiplab() + geom_rootedge()

## without root edge

tree2 <- [Link](text='((A:1,B:2):3,C:2);')
ggtree(tree2) + geom_tiplab() + geom_rootedge()

## setting root edge

geom_rootpoint 33

tree2$[Link] <- 2
ggtree(tree2) + geom_tiplab() + geom_rootedge()

## specify length of root edge for just plotting

## this will ignore tree$[Link]
ggtree(tree2) + geom_tiplab() + geom_rootedge(rootedge = 3)

## For more detailed demonstration of this function, please refer to chapter A.4.5 of
## *Data Integration, Manipulation and Visualization of Phylogenetic Trees*
## <[Link] by Guangchuang Yu.

geom_rootpoint geom_rootpoint

Description
geom_rootpoint is used to add root point layer to a tree

Usage
geom_rootpoint(
mapping = NULL,
data = NULL,
position = "identity",
[Link] = FALSE,
[Link] = NA,
[Link] = TRUE,
...
)

Arguments
mapping Set of aesthetic mapping created by aes(). If [Link] = TRUE, the map-
ping can be inherited from the plot mapping as specified in the call to ggplot().
data The data to be displayed in this layer. If ’NULL’ (the default), the data is inher-
ited from the plot data as specified in the call to ggplot().
position Position adjustment.
[Link] logical. If ’FALSE’ (default), missing values are removed with a warning. If
’TRUE’, missing values are silently removed.
[Link] logical. Should this layer be included in the legends? ’NA’, the default, includes
if any aesthetics are mapped. ’FALSE’ never includes, and ’TRUE’ always
includes.
[Link] logical (defaults to ’TRUE’). If ’FALSE’, overrides the default aesthetics, rather
then combining with them.
... addtional parameters that passed on to this layer. These are often aesthetics,
used to set an aesthetic to a fixed value, like colour = "red" or size = 3.
34 geom_segment2

Details

geom_rootpoint inherit from geom_point2, and it is used to display and customize the points on the
root

Value

root point layer

Author(s)

Guangchuang Yu

References

1. Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in
Bioinformatics. 2020, 69:e96. doi:10.1002/cpbi.96
2. Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping
and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution.
2018, 35(12):3041-3043. doi:10.1093/molbev/msy194
3. Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R
package for visualization and annotation of phylogenetic trees with their covariates and other
associated data. Methods in Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-
210X.12628
For more information, please refer to the online book:Data Integration, Manipulation and Visual-
ization of Phylogenetic Trees.[Link]

See Also

geom_point; geom_rootpoint add point of root; geom_nodepoint add points of internal nodes;
geom_tippoint add points of external nodes (also known as tips or leaves).

Examples
library(ggtree)
tr <- rtree(10)
## add root point
ggtree(tr) + geom_rootpoint()
ggtree(tr) + geom_rootpoint(size=2,color="red",shape=2)

geom_segment2 geom_segment2

Description

geom_segment2 support aes(subset) via setup_data

geom_segment2 35

Usage
geom_segment2(
mapping = NULL,
data = NULL,
stat = "identity",
position = "identity",
lineend = "butt",
[Link] = FALSE,
[Link] = NA,
[Link] = TRUE,
nudge_x = 0,
arrow = NULL,
[Link] = NULL,
...
)

Arguments
mapping Set of aesthetic mappings, defaults to NULL
data A layer specific dataset - only needed if you want to override the plot defaults.
stat Name of stat to modify data.
position The position adjustment to use for overlapping points on this layer.
lineend Line end style, one of butt (default), round and square.
[Link] If "FALSE" (default), missing values are removed with a warning. If "TRUE",
missing values are silently removed, logical.
[Link] Whether to show legend, logical.
[Link] Whether to inherit aesthetic mappings, logical, defaults to "TRUE".
nudge_x adjust the horizontal position of the segments.
arrow specification for arrow heads, as created by arrow().
[Link] fill color to usse for the arrow head (if closed). NULL means use colour aesthetic.
... additional parameter

Details
’geom_segment2’ is a modified version of geom_segment, with subset aesthetic supported

Value
add segment layer

Author(s)
Guangchuang Yu

family "sans" by default, can be any supported font

parse logical, whether to parse labels, if "TRUE", the labels will be parsed into ex-
pressions, defaults to "FALSE"
... additional parameter

Value

ggplot layers

Author(s)

Guangchuang Yu

References

For more detailed demonstration of this function, please refer to chapter 5.2.1 of Data Integration,
Manipulation and Visualization of Phylogenetic Trees [Link]
[Link] by Guangchuang Yu.

Examples
library(ggtree)
tr<- rtree(15)
x <- ggtree(tr)
x + geom_strip(13, 1, color = "red") + geom_strip(3, 7, color = "blue")

geom_striplab geom_striplab

Description

annotate associated taxa (from taxa1 to taxa2, can be Monophyletic, Polyphyletic or Paraphyletc
Taxa) with bar and (optional) text label or image

Usage

geom_striplab(
taxa1 = NULL,
taxa2 = NULL,
label = NULL,
data = NULL,
mapping = NULL,
geom = "text",
parse = FALSE,
...
)
38 geom_striplab

Arguments
taxa1 can be label or node number
taxa2 can be label or node number
label character, character to be showed, when data and mapping is NULL, it is re-
quired.
data [Link], the data to be displayed in the annotation, default is NULL.
mapping Set of aesthetic mappings, default is NULL. The detail see the following expla-
nation.
geom character, one of ’text’, ’label’, ’shadowtext’, ’image’ and ’phylopic’, default is
’text’, and the parameter see the Aesthetics For Specified Geom.
parse logical, whether parse label to emoji font, default is FALSE.
... additional parameters, see also following section.
additional parameters can refer the following parameters. ##’
• offset distance bar and tree, offset of bar and text from the clade, default
is 0.
• [Link] distance bar and text, offset of text from bar, default is 0.
• align logical, whether align clade lab, default is FALSE.
• extend numeric, extend the length of bar, default is 0.
• angle numeric or ’auto’, if angle is auto, the angle of text will be calculated
automatically, which is useful for the circular etc layout, default is 0.
• horizontal logical, whether set label to horizontal, default is TRUE.
• barsize the width of line, default is 0.5.
• barcolour the colour of line, default is ’black’.
• fontsize the size of text, default is 3.88.
• textcolour the colour of text, default is ’black’.
• imagesize the size of image, default is 0.05.
• imagecolor the colour of image, default is NULL, when geom="phylopic",
it should be required.
The parameters also can be set in mapping, when data is provided. Note: the
barsize, barcolour, fontsize, textcolour, imagesize and imagecolor should not be
set in mapping (aesthetics). When the color and size are not be set in mapping,
user can modify them to adjust the attributes of specified geom.

Aesthetics For Specified Geom

geom_striplab() understands the following aesthetics for geom="text"(required aesthetics are in
bold):
• taxa1 selected tip label or tip node, it is required.
• taxa2 selected another tip label or tip node, it is required.
• label labels to be shown, it is required.
• colour the colour of text, default is "black".
• size the size of text, default is 3.88.
• angle the angle of text, default is 0.
• hjust A numeric vector specifying horizontal justification, default is 0.
• vjust A numeric vector specifying vertical justification, default is 0.5.
geom_striplab 39

• alpha the transparency of text, default is NA.

• family the family of text, default is ’sans’.
• fontface the font face of text, default is 1 (plain), others are 2 (bold), 3 (italic), 4 ([Link]).
• lineheight The height of a line as a multiple of the size of text, default is 1.2 .

when the colour, size are not be set in mapping, and user want to modify the colour of text, they
should use textcolour, fontsize to avoid the confusion with bar layer annotation.
geom_striplab() understands the following aesthethics for geom="label" (required aesthetics are
in bold):

• taxa1 selected node to hight light, it is required.

• taxa2 selected another tip label or tip node, it is required.
• label labels to be shown, it is required.
• colour the colour of text, default is "black".
• fill the background colour of the label, default is "white".
• size the size of text, default is 3.88.
• angle the angle of text, default is 0.
• hjust A numeric vector specifying horizontal justification, default is 0.
• vjust A numeric vector specifying vertical justification, default is 0.5.
• alpha the transparency of text, default is NA.
• family the family of text, default is ’sans’.
• fontface the font face of text, default is 1 (plain), others are 2 (bold), 3 (italic), 4 ([Link]).
• lineheight The height of a line as a multiple of the size of text, default is 1.2 .

when the colour, size are not be set in mapping, and user want to modify the colour of text, they
should use textcolour, fontsize to avoid the confusion with bar layer annotation.
geom_striplab() understands the following aesthethics for geom="shadowtext" (required aesthet-
ics are in bold):

• taxa1 selected node to hight light, it is required.

• taxa2 selected another tip label or tip node, it is required.
• label labels to be shown, it is required.
• colour the colour of text, default is "black".
• [Link] the background colour of text, default is ’black’.
• bg.r the width of background text, default is 0.1.
• size the size of text, default is 3.88.
• angle the angle of text, default is 0.
• hjust A numeric vector specifying horizontal justification, default is 0.
• vjust A numeric vector specifying vertical justification, default is 0.5.
• alpha the transparency of text, default is NA.
• family the family of text, default is ’sans’.
• fontface the font face of text, default is 1 (plain), others are 2 (bold), 3 (italic), 4 ([Link]).
• lineheight The height of a line as a multiple of the size of text, default is 1.2 .
40 geom_taxalink

when the colour, size are not be set in mapping, and user want to modify the colour of text, they
should use textcolour, fontsize to avoid the confusion with bar layer annotation.
geom_striplab() understands the following aesthethics for geom="image" or geom="phylopic"
(required aesthetics are in bold):

• taxa1 selected node to hight light, it is required.

• taxa2 selected another tip label or tip node, it is required.
• label labels to be shown, it is required.
• image the image to be annotated, when geom="phylopic", the uid of phylopic databases, it is
required.
• colour the color of image, default is NULL.
• size the size of image, default is 0.05.
• alpha the alpha of image, default is 0.8.

when the colour, size are not be set in mapping, and user want to modify the colour of image, they
should use imagecolour, imagesize to avoid the confusion with bar layer annotation.

Examples

[Link](123)
tr <- rtree(10)
dt <- [Link](ta1=c("t5", "t1"), ta2=c("t6", "t3"), group=c("A", "B"))
p <- ggtree(tr) + geom_tiplab()
p2 <- p +
geom_striplab(
data = dt,
mapping = aes(taxa1 = ta1, taxa2 = ta2,
label = group, color=group),
align = TRUE,
[Link] = FALSE
)
p2

geom_taxalink link between taxa

Description

geom_taxalink supports [Link] as input, the colour, linewidth, linetype and alpha can
be mapped. When the data was provided, the mapping should be also provided, which taxa1 and
taxa2 should be mapped created by aes, aes_ or aes_string. In addition, the hratio, control the
height of curve line, when tree layout is cirular, default is 1. ncp, the number of control points
used to draw the curve, more control points creates a smoother curve, default is 1. They also can be
mapped to a column of data.
geom_taxalink 41

Usage

geom_taxalink(
data = NULL,
mapping = NULL,
taxa1 = NULL,
taxa2 = NULL,
offset = NULL,
outward = "auto",
...
)

Arguments

data [Link], The data to be displayed in this layer, default is NULL.

mapping Set of aesthetic mappings, default is NULL.
taxa1 can be label or node number.
taxa2 can be label or node number.
offset numeric, control the shift of curve line (the ratio of axis value, range is "(0-1)"),
default is NULL.
outward logical, control the orientation of curve when the layout of tree is circular, fan or
other layout in polar coordinate, default is "auto", meaning It will automatically.
... additional parameter.

Value

a list object.

Aesthetics

geom_taxalink() understands the following aesthethics (required aesthetics are in bold):

• taxa1 label or node number of tree.

• taxa2 label or node number of tree.
• group group category of link.
• colour control the color of line, default is black.
• linetype control the type of line, default is 1 (solid).
• linewidth control the width of line, default is 0.5.
• curvature control the curvature of line, default is 0.5, it will be created automatically in polar
coordinate .
• hratio control the height of curve line, default is 1.
• ncp control the smooth of curve line, default is 1.
42 geom_text2

geom_text2 geom_text2

Description
geom_text2 support aes(subset) via setup_data

Usage
geom_text2(
mapping = NULL,
data = NULL,
...,
stat = "identity",
position = "identity",
family = "sans",
parse = FALSE,
[Link] = TRUE,
[Link] = NA,
[Link] = TRUE,
nudge_x = 0,
nudge_y = 0,
check_overlap = FALSE
)

Arguments
mapping the aesthetic mapping
data A layer specific dataset - only needed if you want to override he plot defaults.
... other arguments passed on to ’layer’
stat Name of stat to modify data
position The position adjustment to use for overlapping points on this layer
family sans by default, can be any supported font
parse if TRUE, the labels will be passd into expressions
[Link] logical
[Link] logical
[Link] logical
nudge_x horizontal adjustment
nudge_y vertical adjustment
check_overlap if TRUE, text that overlaps previous text in the same layer will not be plotted

Value
text layer

Author(s)
Guangchuang Yu
geom_tiplab 43

zoom selected clade of a tree

Usage

geom_zoom_clade(node, xexpand = NULL)

Arguments

node internal node number to zoom in its corresponding clade

xexpand numeric, extend x, meaning the ratio of range of the xlim of the original tree,
defaults to NULL.

Details

’geom_zoom_clade’ zooms in on a selected clade of a tree, while showing its on the full view of
tree as a seperated panel for reference

Value

updated tree view

Author(s)

Guangchuang Yu
[Link] 51

[Link] [Link]

Description
path from start node to end node

Usage
[Link](phylo, from, to)

Arguments
phylo phylo object
from start node
to end node

Value
node vectot

Author(s)
Guangchuang Yu

[Link] [Link]

Description
Get the angle between the two nodes specified.

Usage
[Link](df, origin_node_id, node_id)

Arguments
df tree [Link]
origin_node_id origin node id number
node_id end node id number

Value
angle in range [-1, 1], i.e. degrees/180, radians/pi
52 getSubtree

[Link]
[Link]

Description

Get the nodes of tree from root in breadth-first order.

Usage

[Link](df)

Arguments

df tree [Link]

Value

list of node id’s in breadth-first order.

getSubtree getSubtree

Description

Get all children of node from tree, including start_node.

Usage

getSubtree(tree, node)

Arguments

tree ape phylo tree object

node is the tree node id from which the tree is derived.

Value

list of all child node id’s from starting node.

[Link] 53

[Link] [Link]

Description

Get all children of node from df tree using breath-first.

Usage

[Link](df, node)

Arguments

df tree [Link]
node id of starting node.

Value

list of all child node id’s from starting node.

getSubtreeUnrooted getSubtreeUnrooted

Description

Get all subtrees of specified node. This includes all ancestors and relatives of node and return named
list of subtrees.

Usage

getSubtreeUnrooted(tree, node)

Arguments

tree ape phylo tree object

node is the tree node id from which the subtrees are derived.

Value

named list of subtrees with the root id of subtree and list of node id’s making up subtree.
54 getTreeArcAngles

[Link] getSubtreeUnrooted

Description
Get all subtrees of node, as well as remaining branches of parent (ie, rest of tree structure as subtree)
return named list of subtrees with list name as starting node id.

Usage
[Link](df, node)

Arguments
df tree [Link]
node is the tree node id from which the subtrees are derived.

Value
named list of subtrees with the root id of subtree and list of node id’s making up subtree.

getTreeArcAngles getTreeArcAngles

Description
Find the right (clockwise rotation, angle from +ve x-axis to furthest subtree nodes) and left (anti-
clockwise angle from +ve x-axis to subtree) Returning arc angle in [0, 2] (0 to 360) domain.

Usage
getTreeArcAngles(df, origin_id, subtree)

Arguments
df tree [Link]
origin_id node id from which to calculate left and right hand angles of subtree.
subtree named list of root id of subtree (node) and list of node ids for given subtree
(subtree).

Value
named list with right and left angles in range [0,2] i.e 1 = 180 degrees, 1.5 = 270 degrees.
get_clade_position 55

get_clade_position get_clade_position

Description
get position of clade (xmin, xmax, ymin, ymax)

Usage
get_clade_position(treeview, node)

Arguments
treeview tree view
node selected node

Value
[Link]

Author(s)
Guangchuang Yu

get_heatmap_column_position
get_heatmap_column_position

Description
return a [Link] that contains position information for labeling column names of heatmap pro-
duced by gheatmap function

Usage
get_heatmap_column_position(treeview, by = "bottom")

Arguments
treeview output of gheatmap
by one of ’bottom’ or ’top’

Value
[Link]

Author(s)
Guangchuang Yu
56 ggdensitree

get_taxa_name get_taxa_name

Description

get taxa name of a selected node (or tree if node=NULL) sorted by their position in plotting

Usage

get_taxa_name(tree_view = NULL, node = NULL)

Arguments

tree_view tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot object
will be used.
node internal node number to specify a clade. If NULL, using the whole tree

Details

This function extract an ordered vector of the tips from selected clade or the whole tree based on
the ggtree() plot.

Value

ordered taxa name vector

Author(s)

Guangchuang Yu

Examples
tree <- rtree(30)
p <- ggtree(tree)
get_taxa_name(p)

ggdensitree ggdensitree

Description

drawing phylogenetic trees from list of phylo objects

ggdensitree 57

Usage
ggdensitree(
data = NULL,
mapping = NULL,
layout = "slanted",
[Link] = "mode",
[Link] = TRUE,
jitter = 0,
...
)

Arguments
data a list of phylo objects or any object with an [Link] and fortify method
mapping aesthetic mapping
layout one of ’slanted’, ’rectangluar’, ’fan’, ’circular’ or ’radial’ (default: ’slanted’)
[Link] the order of the tips by a character vector of taxa names; or an integer, N, to
order the tips by the order of the tips in the Nth tree; ’mode’ to order the tips
by the most common order; ’mds’ to order the tips based on MDS of the path
length between the tips; or ’mds_dist’ to order the tips based on MDS of the
distance between the tips (default: ’mode’)
[Link] TRUE (default) to align trees by their tips and FALSE to align trees by their root
jitter deviation to jitter tips
... additional parameters passed to fortify, ggtree and geom_tree

Details
The trees plotted by ’ggdensitree()’ will be stacked on top of each other and the structures of the
trees will be rotated to ensure the consistency of the tip order.

Value
tree layer

Author(s)
Yu Guangchuang, Bradley R. Jones

References
For more detailed demonstration of this function, please refer to chapter 4.4.2 of Data Integration,
Manipulation and Visualization of Phylogenetic Trees [Link]
[Link] by Guangchuang Yu.

Examples
require(ape)
require(dplyr)
require(tidyr)

# Plot multiple trees with aligned tips

trees <- list([Link](text="((a:1,b:1):1.5,c:2.5);"), [Link](text="((a:1,c:1):1,b:2);"));
58 ggtree

ggdensitree(trees) + geom_tiplab()

# Plot multiple trees with aligned tips with tip labels and separate tree colors
[Link] <- list(trees[[1]] %>% fortify %>%
mutate(tree="a"), trees[[2]] %>% fortify %>% mutate(tree="b"));
ggdensitree([Link], aes(colour=tree)) + geom_tiplab(colour='black')

# Generate example data

[Link](1)
[Link] <- rmtree(5, 10)
[Link] <- lapply(seq_along([Link]), function(i) {
tree <- [Link][[i]]
tree$[Link] <- paste0("t", 1:10)
dates <- [Link](tree, 1:10, mu=1, nsteps=1)
tree$[Link] <- dates[tree$edge[, 2]] - dates[tree$edge[, 1]]
fortify(tree) %>% mutate(tree=factor(i, levels=[Link](1:10)))
})

# Plot multiple trees with aligned tips from multiple time points
ggdensitree([Link], aes(colour=tree), [Link]=paste0("t", 1:10)) + geom_tiplab(colour='black')

# Read example data

[Link] <- [Link]([Link]("examples", "ggdensitree_example.tree", package="ggtree"))

# Compute OTU
grp <- list(A = c("a.t1", "a.t2", "a.t3", "a.t4"),
B = c("b.t1", "b.t2", "b.t3", "b.t4"),
C = c("c.t1", "c.t2", "c.t3", "c.t4"))
[Link] <- lapply([Link], groupOTU, grp)

# Plot multiple trees colored by OTU

ggdensitree([Link], aes(colour=group), alpha=1/6, [Link]='mds') +
scale_colour_manual(values=c("black", "red", "green", "blue"))

ggtree ggtree

Description
drawing phylogenetic tree from phylo object

Usage
ggtree(
tr,
mapping = NULL,
layout = "rectangular",
[Link] = 0,
mrsd = NULL,
[Link] = FALSE,
yscale = "none",
yscale_mapping = NULL,
ggtree 59

ladderize = TRUE,
right = FALSE,
[Link] = "[Link]",
[Link] = 0,
xlim = NULL,
[Link] = list([Link] = TRUE),
hang = 0.1,
...
)

Arguments
tr phylo object
mapping aesthetic mapping
layout one of ’rectangular’, ’dendrogram’, ’slanted’, ’ellipse’, ’roundrect’, ’fan’, ’cir-
cular’, ’inward_circular’, ’radial’, ’equal_angle’, ’daylight’ or ’ape’
[Link] open angle, only for ’fan’ layout
mrsd most recent sampling date
[Link] logical whether using Date class in time tree
yscale y scale
yscale_mapping yscale mapping for category variable
ladderize logical (default TRUE). Should the tree be re-organized to have a ’ladder’ aspect?
right logical. If ladderize = TRUE, should the ladder have the smallest clade on the
right-hand side? See ape::ladderize() for more information.
[Link] variable for scaling branch, if ’none’ draw cladogram
[Link] position of the root node (default = 0)
xlim x limits, only works for ’inward_circular’ layout
[Link] list, the parameters of layout, when layout is a function. [Link]=TRUE and
layout is a function, the coordinate will be re-calculated as a igraph object, if
[Link]=FALSE and layout, the coordinate will be re-calculated keep original
object phylo or treedata.
hang numeric The fraction of the tree plot height by which labels should hang below
the rest of the plot. A negative value will cause the labels to hang down from 0.
This parameter only work with the ’dendrogram’ layout for ’hclust’ like class,
default is 0.1.
... additional parameter
some dot arguments:
• nsplit integer, the number of branch blocks divided when ’continuous’ is
not "none", default is 200.

Value
tree

Author(s)
Yu Guangchuang
60 gheatmap

References
1. G Yu, TTY Lam, H Zhu, Y Guan (2018). Two methods for mapping and visualizing associated
data on phylogeny using ggtree. Molecular Biology and Evolution, 35(2):3041-3043. https:
//[Link]/10.1093/molbev/msy194
2. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam (2017). ggtree: an R package for visualization
and annotation of phylogenetic trees with their covariates and other associated data. Methods
in Ecology and Evolution, 8(1):28-36. [Link]
For more information, please refer to Data Integration, Manipulation and Visualization of Phylo-
genetic Trees [Link] by Guangchuang Yu.

gzoom gzoom method

Description
gzoom method
gzoom method
zoom selected subtree

Usage
gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...)

## S4 method for signature 'ggtree'

gzoom(object, focus, widths = c(0.3, 0.7), xmax_adjust = 0)

## S4 method for signature 'treedata'

gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7))

## S4 method for signature 'phylo'

gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7))

Arguments
object supported tree objects
focus selected tips
subtree logical
widths widths
... additional parameter
xmax_adjust adjust xmax (xlim[2])

Value
figure

[Link] gzoom

Description
plots simultaneously a whole phylogenetic tree and a portion of it.

Usage
[Link](phy, focus, subtree = FALSE, widths = c(0.3, 0.7))
hexpand 63

Arguments
phy phylo object
focus selected tips
subtree logical
widths widths

Value
a list of ggplot object

Author(s)
ygc

hexpand hexpand

Description
hexpand
vexpand
expand xlim (ylim) by ratio of x (y) axis range

Usage
hexpand(ratio, direction = 1)

vexpand(ratio, direction = 1)

ggexpand(ratio, direction = 1, side = "hv")

Arguments
ratio expand x (y) axis limits by amount of xrange (yrange) * ratio
direction expand x axis limit at right hand side if direction is 1 (default), or left hand side
if direction is -1
side one of ’h’ for horizontal and ’v’ for vertical or ’hv’ for both (default).

Value
ggexpand object

Author(s)
Guangchuang Yu

Examples
x <- rtree(20)
x$[Link] <- paste0('RRRRREEEEEAAAAALLLLLYYYYY_Long_Lable_', x$[Link])
p1 <- ggtree(x) + geom_tiplab()
p1 + ggexpand(1.5, side = "h")
64 layoutDaylight

label_pad Padding taxa labels

Description
This function adds padding characters to the left side of taxa labels, adjust their length to the longest
label.

Usage
label_pad(label, justify = "right", pad = "·")

Arguments
label taxa label
justify should a character vector be right-justified (default), left-justified, centred or left
alone.
pad padding character (defaults to dots)

Value
Taxa labels with padding characters added

Author(s)
Guangchuang Yu and Yonghe Xia

References
[Link]

Examples
library(ggtree)
[Link](2015-12-21)
tree <- rtree(5)
tree$[Link][2] <- "long string for test"
label_pad(tree$[Link])

layoutDaylight Equal daylight layout method for unrooted trees.

Description
#’ @title

Usage
layoutDaylight(model, [Link], MAX_COUNT = 5)
layoutEqualAngle 65

Arguments
model tree object, e.g. phylo or treedata
[Link] set to ’none’ for edge length of 1. Otherwise the phylogenetic tree edge length
is used.
MAX_COUNT the maximum number of iterations to run (default 5)

Value
tree as [Link] with equal angle layout.

References
The following aglorithm aims to implement the vague description of the "Equal-daylight Algo-
rithm" in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.

Leafs are subtrees with no children

Initialise tree using equal angle algorithm
tree_df = equal_angle(tree)

nodes = get list of nodes in tree_df breadth-first

nodes = remove tip nodes.

layoutEqualAngle layoutEqualAngle

Description
’Equal-angle layout algorithm for unrooted trees’

Usage
layoutEqualAngle(model, [Link] = "[Link]")

Arguments
model tree object, e.g. phylo or treedata
[Link] set to ’none’ for edge length of 1. Otherwise the phylogenetic tree edge length
is used.

Value
tree as [Link] with equal angle layout.

References
"Inferring Phylogenies" by Joseph Felsenstein.
66 layout_rectangular

layout_rectangular layout_rectangular

Description
transform circular/fan layout to rectangular layout
transform rectangular layout to circular layout
transform rectangular/circular layout to inward circular layout
transform rectangular/circular layout to fan layout
transform rectangular layout to dendrogram layout

Usage
layout_rectangular()

layout_circular()

layout_inward_circular(xlim = NULL)

layout_fan(angle = 180)

layout_dendrogram()

Arguments
xlim setting x limits, which will affect the center space of the tree
angle open tree at specific angle

Author(s)
Guangchuang Yu

Examples
tree <- rtree(20)
p <- ggtree(tree, layout = "circular") + layout_rectangular()
tree <- rtree(20)
p <- ggtree(tree)
p + layout_circular()
tree <- rtree(20)
p <- ggtree(tree)
p + layout_inward_circular(xlim=4) + geom_tiplab(hjust=1)
tree <- rtree(20)
p <- ggtree(tree)
p + layout_fan(angle=90)
tree <- rtree(20)
p <- ggtree(tree)
p + p + layout_dendrogram()
msaplot 67

msaplot msaplot

Description
visualize phylogenetic tree with multiple sequence alignment

Usage
msaplot(
p,
fasta,
offset = 0,
width = 1,
color = NULL,
window = NULL,
bg_line = TRUE,
height = 0.8
)

Arguments
p tree view
fasta fasta file that contains multiple sequence alignment information
offset set the offset of MSA to tree
width total width of alignment, compare to width of tree, defaults to 1, which means
they are of the same length
color set color of the tree
window specific a slice of alignment to display
bg_line whether to add background line in alignment, defaults to "TRUE"
height height ratio of sequence, defaults to 0.8

Value
tree view

Author(s)
Guangchuang Yu

References
For demonstration of this function, please refer to chapter 7.4 of Data Integration, Manipulation
and Visualization of Phylogenetic Trees [Link]
by Guangchuang Yu.
68 nodebar

multiplot multiplot

Description
plot multiple ggplot objects in one page

Usage
multiplot(
...,
plotlist = NULL,
ncol,
widths = rep_len(1, ncol),
labels = NULL,
label_size = 5
)

Arguments
... plots
plotlist plot list
ncol set the number of column to display the plots
widths the width of each plot
labels set labels for labeling the plots
label_size set font size of the label

Value
plot

Author(s)
Guangchuang Yu

nodebar nodebar

Description
generate a list of bar charts for results of ancestral state reconstruction

Usage
nodebar(data, cols, color, alpha = 1, position = "stack")
nodepie 69

Arguments
data a [Link] of stats with an additional column of node number named "node"
cols columns of the [Link] that store the stats
color set color of bars
alpha set transparency of the charts
position position of bars, if ’stack’ (default) make bars stacked atop one another, ’dodge’
make them dodged side-to-side

Value
list of ggplot objects

Author(s)
Guangchuang Yu

nodepie nodepie

Description
generate a list of pie charts for results of ancestral stat reconstruction

Usage
nodepie(
data,
cols,
color,
alpha = 1,
[Link] = "transparent",
[Link] = 0
)

Value
list of ggplot objects

Author(s)
Guangchuang Yu
70 range_format

open_tree open_tree

Description
transform a tree in either rectangular or circular layout into the fan layout that opens with a specific
angle

Usage
open_tree(treeview, angle)

Arguments
treeview tree view in rectangular/circular layout
angle open the tree at a specific angle

Value
updated tree view

Author(s)
Guangchuang Yu

Examples
tree <- rtree(15)
p <- ggtree(tree) + geom_tiplab()
open_tree(p, 180)

range_format range_format

Description
format a list of range (HPD, CI, etc that has length of 2)

Usage
range_format(x, trans = NULL)

Arguments
x input list
trans transformation function

Value
character vector of [lower, upper]
reexports 71

Author(s)
Guangchuang Yu

reexports Objects exported from other packages

Description
These objects are imported from other packages. Follow the links below to see their documentation.

ape [Link], rtree

aplot plot_list
dplyr collapse
ggfun %<+%, identify, td_filter, td_mutate, td_unnest
ggplot2 aes, fortify, geom_label, geom_point, geom_text, ggplot, ggsave, guide_legend,
margin, scale_color_manual, scale_colour_manual, scale_fill_manual, scale_x_continuous,
theme, xlim
grid arrow, unit
magrittr %>%
tidytree groupClade, groupOTU, MRCA, nodeid, nodelab

Examples
nwk <- [Link]("extdata", "[Link]", package="treeio")
tree <- [Link](nwk)
p <- ggtree(tree)
dd <- [Link](taxa=LETTERS[1:13],
place=c(rep("GZ", 5), rep("HK", 3), rep("CZ", 4), NA),
value=round(abs(rnorm(13, mean=70, sd=10)), digits=1))
[Link](dd) <- NULL
p %<+% dd + geom_text(aes(color=place, label=label), hjust=-0.5)

revts revts

Description
reverse timescle x-axis by setting the most recent tip to 0

Usage
revts(treeview)

Arguments
treeview original tree view
72 rotate

Details
’scale_x_continuous(labels=abs)’ is required if users want to set the x-axis lable to absolute value

Value
updated tree view

Author(s)
Guangchuang Yu

Examples
tr <- rtree(10)
p <- ggtree(tr) + theme_tree2()
p2 <- revts(p)
p2 + scale_x_continuous(labels=abs)

rotate rotate

Description
rotate selected clade by 180 degree

Usage
rotate(tree_view = NULL, node)

Arguments
tree_view tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot object
will be used.
node internal node number to specify a clade. If NULL, using the whole tree

Value
ggplot2 object

Author(s)
Guangchuang Yu

Examples
x <- rtree(15)
p <- ggtree(x) + geom_tiplab()
rotate(p, 17)
[Link] 73

[Link] [Link]

Description
Rotate the points in a tree [Link] around a pivot node by the angle specified.

Usage
[Link](df, pivot_node, nodes, angle)

Arguments
df tree [Link]
pivot_node is the id of the pivot node.
nodes list of node numbers that are to be rotated by angle around the pivot_node
angle in range [0,2], ie degrees/180, radians/pi

Value
updated tree [Link] with points rotated by angle

rotate_tree rotate_tree

Description
rotate circular tree in a certain angle

Usage
rotate_tree(treeview, angle)

Arguments
treeview tree view in circular layout
angle the angle of rotation

Value
updated tree view

Author(s)
Guangchuang Yu

Examples
tree <- rtree(15)
p <- ggtree(tree) + geom_tiplab()
p2 <- open_tree(p, 180)
rotate_tree(p2, 180)
74 scale_color

scaleClade scaleClade

Description

zoom out/in a selected clade to emphasize or de-emphasize it

Usage

scaleClade(tree_view = NULL, node, scale = 1, vertical_only = TRUE)

Arguments

tree_view tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot object
will be used.
node internal node number to specify a clade. If NULL, using the whole tree
scale the scale of the selected clade. The clade will be zoom in when scale > 1, and
will be zoom out when scale < 1
vertical_only logical. If TRUE (default), only vertical will be scaled. If FALSE, the clade will
be scaled vertical and horizontally.

Value

tree view

Author(s)

Guangchuang Yu

Examples
x <- rtree(15)
p <- ggtree(x) + geom_tiplab() +
geom_nodelab(aes(subset=!isTip, label=node), hjust = -.1, color = "red")
scaleClade(p, 24, scale = .1)

scale_color scale_color method

Description

scale_color method
scale color by a numerical tree attribute
scale_color_subtree 75

Usage

scale_color(object, by, ...)

## S4 method for signature 'treedata'

scale_color(object, by, ...)

## S4 method for signature 'phylo'

scale_color(object, by, ...)

Arguments

object treedata object

by one of numerical attributes
... additional parameter

Value

color vector

scale_color_subtree scale_color_subtree

Description

scale tree color by subtree (e.g., output of cutree, kmeans, or other clustering algorithm)

Usage

scale_color_subtree(group)

scale_colour_subtree(group)

Arguments

group taxa group information

Value

updated tree view

Author(s)

Guangchuang Yu
76 scale_x_range

scale_x_ggtree scale_x_ggtree

Description
scale x for tree with gheatmap

Usage
scale_x_ggtree(breaks = waiver(), labels = waiver())

Arguments
breaks set breaks for tree
labels lables for corresponding breaks

Details
Since setting x-axis for tree with gheatmap by using ’theme_tree2()’ is quite tricky, ’scale_x_ggtree’
can help set the x-axis more reasonably.

Value
updated tree view

Author(s)
Guangchuang Yu

References
For more detailed demonstration of this function, please refer to chapter 7.3 of Data Integration,
Manipulation and Visualization of Phylogenetic Trees [Link]
[Link] by Guangchuang Yu.

scale_x_range scale_x_range

Description
add second x-axis for geom_range

Usage
scale_x_range()

Details
notice that the first axis is disabled in the default theme thus users need to enable it first before using
scale_x_range
set_hilight_legend 77

Value
ggtree object

Author(s)
Guangchuang Yu

References
For demonstration of this function ,please refer to chapter 5.2.4 of Data Integration, Manipulation
and Visualization of Phylogenetic Trees [Link]
by Guangchuang Yu.

set_hilight_legend set_hilight_legend

Description
set legend for multiple geom_hilight layers

Usage
set_hilight_legend(p, color, label, alpha = 1)

Arguments
p ggtree object
color color vector
label label vector
alpha transparency of color

Value
updated ggtree object

Author(s)
Guangchuang Yu

StatBalance StatBalance

Description
StatBalance
78 theme_inset

theme_dendrogram theme_dendrogram

Description
dendrogram theme

Usage
theme_dendrogram(bgcolor = "white", fgcolor = "black", ...)

Arguments
bgcolor set background color, defaults to "white"
fgcolor set color of axis
... additional parameter

Author(s)
Guangchuang Yu

theme_inset theme_inset

Description
inset theme

Usage
theme_inset([Link] = "none", ...)

Arguments
[Link]
set the position of legend
... additional parameter

Details
theme for inset function

Value
ggplot object

Author(s)
Guangchuang Yu
theme_tree 79

theme_tree theme_tree

Description
tree theme

Usage
theme_tree(bgcolor = "white", ...)

Arguments
bgcolor set background color, defaults to "white"
... additional parameter

Details
’theme_tree’ defines a blank background to display tree

Value
updated ggplot object with new theme

Author(s)
Guangchuang Yu

Examples
require(ape)
tr <- rtree(10)
ggtree(tr) + theme_tree()

theme_tree2 theme_tree2

Description
tree2 theme

Usage
theme_tree2(bgcolor = "white", fgcolor = "black", ...)

Arguments
bgcolor set background color, defaults to "white"
fgcolor set foreground color, defaults to "black"
... additional parameter
80 viewClade

Details
’theme_tree2’ supports displaying phylogenetic distance by setting x-axis

Value
updated ggplot object with new theme

Author(s)
Guangchuang Yu

Examples
require(ape)
tr <- rtree(10)
ggtree(tr) + theme_tree2()

viewClade viewClade

Description
view a selected clade of tree, clade can be selected by specifying a node number or determined by
the most recent common ancestor of selected tips

Usage
viewClade(tree_view = NULL, node, xmax_adjust = 0)

Arguments
tree_view tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot object
will be used.
node internal node number to specify a clade. If NULL, using the whole tree
xmax_adjust adjust the max range of x axis

Value
clade plot

Author(s)
Guangchuang Yu

Examples
x <- rtree(15)
p <- ggtree(x) + geom_tiplab()
viewClade(p, 18, xmax_adjust = 0.)
xlim_expand 81

xlim_expand xlim_expand

Description
expand x axis limits for specific panel

Usage
xlim_expand(xlim, panel)

Arguments
xlim x axis limits
panel name of the panel to expand

Value
updated tree view

Author(s)
Guangchuang Yu

Examples
x <- rtree(30)
p <- ggtree(x) + geom_tiplab()
d <- [Link](label = x$[Link],
value = rnorm(30))
p2 <- p + geom_facet(panel = "Dot", data = d,
geom = geom_point, mapping = aes(x = value))
p2 + xlim_expand(c(-10, 10), 'Dot')

xlim_tree xlim_tree

Description
set x axis limits specially for Tree panel

Usage
xlim_tree(xlim)

Arguments
xlim x axis limits
82 zoomClade

Value
updated tree view

Author(s)
Guangchuang Yu

zoomClade zoomClade

Description
zoom in on a selected clade of a tree, while showing its on the full view of tree as a seperated panel
for reference

Usage
zoomClade(tree_view = NULL, node, xexpand = NULL)

Value
full tree with zoom in clade

Author(s)
Guangchuang Yu

Examples
## Not run:
x <- rtree(15)
p <- ggtree(x) + geom_tiplab() +
geom_nodelab(aes(subset=!isTip, label=node), hjust = -.1, color = "red")
zoomClade(p, 21, xexpand = .2)

## End(Not run)
%+>% 83

%+>% %+>%

Description
update data with tree info (y coordination and panel)

Usage
p %+>% .data

Arguments
p tree view
.data [Link]

Details
add tree information to an input data. This function will setup y coordination and panel info for
data used in facet_plot and geom_faceet

Value
updated [Link]

Author(s)
Guangchuang Yu

%<% %<%

Description
update tree

Usage
pg %<% x

Arguments
pg ggtree object
x tree object
84 %<%

Details
This operator apply the visualization directives in ggtree object (lhs) to visualize another tree object
(rhs), that is similar to Format Painter.

Value
updated ggplot object

Author(s)
Guangchuang Yu

Examples
library("ggplot2")
nwk <- [Link]("extdata", "[Link]", package="treeio")
tree <- [Link](nwk)
p <- ggtree(tree) + geom_tippoint(color="#b5e521", alpha=1/4, size=10)
p %<% rtree(30)
Index

∗ datasets geom_hilight, 20
StatBalance, 77 geom_inset, 22
∗ internal geom_label, 25, 71
ggtree-package, 4 geom_label (reexports), 71
reexports, 71 geom_label2, 23
%<+% (reexports), 71 geom_motif, 25
%>% (reexports), 71 geom_nodelab, 26
%+>%, 83 geom_nodelab2, 27
%<+%, 71 geom_nodepoint, 27, 30, 34
%<%, 83 geom_point, 30, 34, 71
%>%, 71 geom_point (reexports), 71
geom_point2, 29
add_colorbar, 5
geom_range, 31
aes, 71
geom_rootedge, 32
aes (reexports), 71
geom_rootpoint, 30, 33, 34
ape::ladderize(), 59
geom_segment, 35
applyLayoutDaylight, 5
geom_segment2, 34
arrow, 71
geom_strip, 36
arrow (reexports), 71
geom_striplab, 37
[Link], 6
geom_taxalink, 40
collapse, 71 geom_text, 43, 71
collapse (reexports), 71 geom_text (reexports), 71
[Link], 6 geom_text2, 42
geom_tiplab, 43, 46
Date2decimal, 7 geom_tiplab(), 26, 27
decimal2Date, 8 geom_tiplab2, 45
geom_tippoint, 30, 34, 46
expand, 8 geom_tree, 47
geom_tree(), 60
facet_data, 9
geom_tree2, 48
facet_labeller, 9
geom_treescale, 49
facet_plot, 10
geom_zoom_clade, 50
facet_widths, 11
flip, 11 [Link], 51
fortify, 71 get_clade_position, 55
fortify (reexports), 71 get_heatmap_column_position, 55
get_taxa_name, 56
geom_aline, 12 [Link], 51
geom_balance, 13 [Link], 52
geom_cladelab, 14 getSubtree, 52
geom_cladelabel, 17, 19 [Link], 53
geom_cladelabel2, 18, 18 getSubtreeUnrooted, 53
geom_facet (facet_plot), 10 [Link], 54
geom_highlight (geom_hilight), 20 getTreeArcAngles, 54

85
86 INDEX

ggdensitree, 56 package-ggtree (ggtree-package), 4

ggexpand (hexpand), 63 plot_list, 71
ggplot, 71 plot_list (reexports), 71
ggplot (reexports), 71
ggsave, 71 range_format, 70
ggsave (reexports), 71 [Link], 71
ggtree, 58 [Link] (reexports), 71
ggtree-package, 4 reexports, 71
gheatmap, 60 revts, 71
groupClade, 71 rotate, 72
groupClade (reexports), 71 rotate_tree, 73
groupOTU, 71 [Link], 73
groupOTU (reexports), 71 rtree, 71
guide_legend, 71 rtree (reexports), 71
guide_legend (reexports), 71
scale_color, 74
gzoom, 62
scale_color,phylo-method (scale_color),
gzoom,ggtree-method (gzoom), 62
74
gzoom,phylo-method (gzoom), 62
scale_color,treedata-method
gzoom,treedata-method (gzoom), 62
(scale_color), 74
[Link], 62
scale_color_manual, 71
scale_color_manual (reexports), 71
hexpand, 63
scale_color_subtree, 75
scale_colour_manual, 71
identify, 71
scale_colour_manual (reexports), 71
identify (reexports), 71
scale_colour_subtree
inset (geom_inset), 22
(scale_color_subtree), 75
label_pad, 64 scale_fill_manual, 71
layout_circular (layout_rectangular), 66 scale_fill_manual (reexports), 71
layout_dendrogram (layout_rectangular), scale_x_continuous, 71
66 scale_x_continuous (reexports), 71
layout_fan (layout_rectangular), 66 scale_x_ggtree, 76
scale_x_range, 76
layout_inward_circular
scaleClade, 74
(layout_rectangular), 66
set_hilight_legend, 77
layout_rectangular, 66
StatBalance, 77
layoutDaylight, 64
layoutEqualAngle, 65 td_filter, 71
td_filter (reexports), 71
margin, 71 td_mutate, 71
margin (reexports), 71 td_mutate (reexports), 71
MRCA, 71 td_unnest, 71
MRCA (reexports), 71 td_unnest (reexports), 71
msaplot, 67 theme, 71
multiplot, 68 theme (reexports), 71
theme_dendrogram, 78
nodebar, 68
theme_inset, 78
nodeid, 71
theme_tree, 79
nodeid (reexports), 71 theme_tree2, 79
nodelab, 71
nodelab (reexports), 71 unit, 71
nodepie, 69 unit (reexports), 71

open_tree, 70 vexpand (hexpand), 63

INDEX 87

viewClade, 80

xlim, 71
xlim (reexports), 71
xlim_expand, 81
xlim_tree, 81

zoomClade, 82

ggtree xlim_tree Function Overview
No ratings yet
ggtree xlim_tree Function Overview
59 pages
ggplot2: R Graphics Grammar Package
No ratings yet
ggplot2: R Graphics Grammar Package
180 pages
Package Ggplot2': October 25, 2018
No ratings yet
Package Ggplot2': October 25, 2018
222 pages
ggalt: Enhanced Geometries for ggplot2
No ratings yet
ggalt: Enhanced Geometries for ggplot2
33 pages
Ggplot2 PDF
No ratings yet
Ggplot2 PDF
304 pages
ggplot2: Economics Data Analysis
No ratings yet
ggplot2: Economics Data Analysis
215 pages
Terra Package: Spatial Data Errors
No ratings yet
Terra Package: Spatial Data Errors
324 pages
Ternary Diagrams with ggtern Package
No ratings yet
Ternary Diagrams with ggtern Package
104 pages
Spatial Data Analysis with Terra Package
No ratings yet
Spatial Data Analysis with Terra Package
367 pages
Terra
No ratings yet
Terra
383 pages
Plotrix
No ratings yet
Plotrix
231 pages
Plotrix
No ratings yet
Plotrix
231 pages
ggplot2 R: Complete Customization Guide
No ratings yet
ggplot2 R: Complete Customization Guide
31 pages
Circle Resizing with Key Events
No ratings yet
Circle Resizing with Key Events
355 pages
Spatial Data Analysis with Terra
No ratings yet
Spatial Data Analysis with Terra
8 pages
Social Network Analysis Tools in R
No ratings yet
Social Network Analysis Tools in R
187 pages
Simplify ggplot2 Visualizations with ggblanket
No ratings yet
Simplify ggplot2 Visualizations with ggblanket
195 pages
Terra Package for Spatial Analysis
No ratings yet
Terra Package for Spatial Analysis
369 pages
Geographic Data Analysis with R Raster
No ratings yet
Geographic Data Analysis with R Raster
229 pages
Spatial Data Classes and Methods
No ratings yet
Spatial Data Classes and Methods
121 pages
Geographic Data Analysis Package
No ratings yet
Geographic Data Analysis Package
246 pages
Visualizing Spatial Data with ggmap
No ratings yet
Visualizing Spatial Data with ggmap
70 pages
Interactive Graphics with Plotly
No ratings yet
Interactive Graphics with Plotly
72 pages
R igraph Package for Network Analysis
No ratings yet
R igraph Package for Network Analysis
426 pages
Visualize Phylogenetic Trees with ggtreeExtra
No ratings yet
Visualize Phylogenetic Trees with ggtreeExtra
17 pages
The R Development Core Team-R Reference Manual - Base Package, Vol. 2-Network Theory Ltd. (2003) PDF
No ratings yet
The R Development Core Team-R Reference Manual - Base Package, Vol. 2-Network Theory Ltd. (2003) PDF
704 pages
Spatial Dependence for Simple Features
No ratings yet
Spatial Dependence for Simple Features
68 pages
Network Analysis with igraph in R
No ratings yet
Network Analysis with igraph in R
475 pages
Color Blind Friendly ggplot Themes
No ratings yet
Color Blind Friendly ggplot Themes
81 pages
The Matplotlib User's Guide
No ratings yet
The Matplotlib User's Guide
868 pages
GEOS R API for Geometry Processing
No ratings yet
GEOS R API for Geometry Processing
38 pages
Topographic and Geologic Mapping Tool
No ratings yet
Topographic and Geologic Mapping Tool
185 pages
Package Ggridges': R Topics Documented
No ratings yet
Package Ggridges': R Topics Documented
27 pages
Ggbio
No ratings yet
Ggbio
266 pages
Lattice: Trellis Graphics for R
No ratings yet
Lattice: Trellis Graphics for R
159 pages
Terra: Spatial Data Analysis Tools
No ratings yet
Terra: Spatial Data Analysis Tools
218 pages
Visualize BART Models in R
No ratings yet
Visualize BART Models in R
40 pages
Seurat: Single Cell Genomics Tools
No ratings yet
Seurat: Single Cell Genomics Tools
212 pages
GCDkit: Geochemical Data Toolkit
No ratings yet
GCDkit: Geochemical Data Toolkit
175 pages
R Tools for Malaria Data Analysis
No ratings yet
R Tools for Malaria Data Analysis
42 pages
Phylogenetic Tools for R Analysis
100% (1)
Phylogenetic Tools for R Analysis
132 pages
Microarray Analysis Tool: genArise
No ratings yet
Microarray Analysis Tool: genArise
34 pages
Statistical Analysis Package HH
No ratings yet
Statistical Analysis Package HH
292 pages
Genetic Map Construction in R
No ratings yet
Genetic Map Construction in R
71 pages
Package Maptools': January 30, 2016
No ratings yet
Package Maptools': January 30, 2016
81 pages
GSC Geochemistry EDA Package
No ratings yet
GSC Geochemistry EDA Package
209 pages
Meaning of 'R' in tracem-p
100% (1)
Meaning of 'R' in tracem-p
94 pages
Circular Visualization with circlize in R
No ratings yet
Circular Visualization with circlize in R
171 pages
Spatial Data Manipulation Tools
No ratings yet
Spatial Data Manipulation Tools
83 pages
Statistical Analysis Package HH
No ratings yet
Statistical Analysis Package HH
124 pages
Species Distribution Modeling in R
No ratings yet
Species Distribution Modeling in R
156 pages
Data Visualization With Ggplot2::: Cheat Sheet
No ratings yet
Data Visualization With Ggplot2::: Cheat Sheet
2 pages
Spatial Analysis Tools in R
100% (1)
Spatial Analysis Tools in R
119 pages
Microarray Data Analysis Tool
No ratings yet
Microarray Data Analysis Tool
34 pages
Simple Features Package for R
No ratings yet
Simple Features Package for R
128 pages
R Package for Phylogenetic Tree Data
100% (1)
R Package for Phylogenetic Tree Data
31 pages
R Admin
No ratings yet
R Admin
80 pages
R-4.3.3 Windows Installation Guide
No ratings yet
R-4.3.3 Windows Installation Guide
23 pages
Local Community: Pronunciation & Vocabulary Guide
No ratings yet
Local Community: Pronunciation & Vocabulary Guide
10 pages
Troubleshooting Baldor Air Compressors
No ratings yet
Troubleshooting Baldor Air Compressors
5 pages
Mechanical Engineering Exam: Refrigeration & AC
No ratings yet
Mechanical Engineering Exam: Refrigeration & AC
17 pages
Kamala Das: The Looking Glass Analysis
No ratings yet
Kamala Das: The Looking Glass Analysis
10 pages
UK Biotechnology Sector Updates 2012
No ratings yet
UK Biotechnology Sector Updates 2012
34 pages
Sharda Cropchem Ltd: 2018 Company Update
No ratings yet
Sharda Cropchem Ltd: 2018 Company Update
12 pages
Suction Rolls in Paper Machines Training
100% (1)
Suction Rolls in Paper Machines Training
26 pages
Specialized Cell Project Guide
No ratings yet
Specialized Cell Project Guide
3 pages
Housing Strategies and Approaches Overview
No ratings yet
Housing Strategies and Approaches Overview
8 pages
CE133: Reinforced/Prestressed Concrete Syllabus
No ratings yet
CE133: Reinforced/Prestressed Concrete Syllabus
6 pages
Turmeric Honey for Chronic Wound Healing
No ratings yet
Turmeric Honey for Chronic Wound Healing
6 pages
Anaesthetic Aspects of Stereotactic Brain Biopsy
No ratings yet
Anaesthetic Aspects of Stereotactic Brain Biopsy
4 pages
wow
No ratings yet
wow
10 pages
Step-by-Step Isometric Drawing Guide
No ratings yet
Step-by-Step Isometric Drawing Guide
56 pages
Smart Helmet Detection Ignition System
No ratings yet
Smart Helmet Detection Ignition System
3 pages
Soybean Growth in Agroforestry Systems
No ratings yet
Soybean Growth in Agroforestry Systems
11 pages
Market Inefficiency of Negative Externalities
100% (1)
Market Inefficiency of Negative Externalities
10 pages
Biomass Pyrolysis: Methods and Applications
No ratings yet
Biomass Pyrolysis: Methods and Applications
50 pages
Driven vs Bored Cast-in-Situ Piles
No ratings yet
Driven vs Bored Cast-in-Situ Piles
17 pages
AI Image Processing Seminar Report
No ratings yet
AI Image Processing Seminar Report
15 pages
Modern Physics Practical Exam Guide
No ratings yet
Modern Physics Practical Exam Guide
4 pages
Volume 11, Issue 1
No ratings yet
Volume 11, Issue 1
54 pages
2008 Scion xB Exhaust System Guide
No ratings yet
2008 Scion xB Exhaust System Guide
10 pages
Conflict Over Artistic Representation
No ratings yet
Conflict Over Artistic Representation
3 pages
Harmonics and The Glass Bead Game: Peter Neubäcker
100% (1)
Harmonics and The Glass Bead Game: Peter Neubäcker
27 pages
Automobile Engineering Lab Guide
No ratings yet
Automobile Engineering Lab Guide
31 pages
Sample Graduation Test 17 Format
100% (1)
Sample Graduation Test 17 Format
10 pages
API-653 Exam Preparation Guide
100% (22)
API-653 Exam Preparation Guide
288 pages
NSIC Registered Rice Varieties 2022
No ratings yet
NSIC Registered Rice Varieties 2022
98 pages
Chilli Powder Product Specification
No ratings yet
Chilli Powder Product Specification
6 pages