ggtree: ggtree – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

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",
  root.position = 0,
  xlim = NULL,
  ...
)

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
`...`	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

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
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

Examples

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

ggtree

an R package for visualization of tree and annotation data

v2.4.2

Artistic-2.0

Authors

Guangchuang Yu [aut, cre, cph] (<https://orcid.org/0000-0002-6485-8781>), Tommy Tsan-Yuk Lam [aut, ths], Shuangbin Xu [aut] (<https://orcid.org/0000-0003-3513-5362>), Yonghe Xia [ctb], Justin Silverman [ctb], Bradley Jones [ctb], Watal M. Iwasaki [ctb], Ruizhu Huang [ctb]

Initial release

ggtree

Description

Usage

Arguments

Value

Author(s)

References

See Also

Examples

ggtree

We don't support your browser anymore