ggtree {ggtree}R Documentation

visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics ggtree provides functions for visualizing phylogenetic tree and its associated data in R.

Description

If you use ggtree in published research, please cite: 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

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", ...)

Arguments

tr

phylo object

mapping

aesthetic mapping

layout

one of 'rectangular', 'slanted', 'fan', 'circular', 'radial', 'equal_angle' or 'daylight'

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 ladderize for more information.

branch.length

variable for scaling branch, if 'none' draw cladogram

...

additional parameter

Value

tree

Author(s)

Yu Guangchuang

See Also

ladderize

Examples

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

[Package ggtree version 1.16.0 Index]