ggtree {ggtree} | R Documentation |
ggtree
provides functions for visualizing phylogenetic tree and its associated data in R.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
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, ... )
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 |
right |
logical. If |
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:
|
tree
Yu Guangchuang
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
require(ape) tr <- rtree(10) ggtree(tr)