ggtree: ggtree

In YuLab-SMU/ggtree: an R package for visualization of tree and annotation data

ggtree

Description

drawing phylogenetic tree from phylo object

Usage

ggtree(
  tr,
  mapping = NULL,
  layout = "rectangular",
  open.angle = 0,
  mrsd = NULL,
  as.Date = FALSE,
  yscale = "none",
  yscale_mapping = NULL,
  ladderize = TRUE,
  right = FALSE,
  branch.length = "branch.length",
  root.position = 0,
  xlim = NULL,
  layout.params = list(as.graph = TRUE),
  hang = 0.1,
  ...
)

Arguments

tr	phylo object
mapping	aesthetic mapping
layout	one of 'rectangular', 'dendrogram', 'slanted', 'ellipse', 'roundrect', 'fan', 'circular', 'inward_circular', 'radial', 'equal_angle', 'daylight' or 'ape'
open.angle	open angle, only for 'fan' layout
mrsd	most recent sampling date
as.Date	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.
branch.length	variable for scaling branch, if 'none' draw cladogram
root.position	position of the root node (default = 0)
xlim	x limits, only works for 'inward_circular' layout
layout.params	list, the parameters of layout, when layout is a function. as.graph=TRUE and layout is a function, the coordinate will be re-calculated as a igraph object, if as.graph=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

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://doi.org/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. https://doi.org/10.1111/2041-210X.12628

For more information, please refer to Data Integration, Manipulation and Visualization of Phylogenetic Trees http://yulab-smu.top/treedata-book/index.html by Guangchuang Yu.

See Also

geom_tree()

Examples

require(ape) 
tr <- rtree(10)
ggtree(tr)

YuLab-SMU/ggtree documentation built on Nov. 3, 2024, 4:15 p.m.