geom_rootedge: geom_rootedge

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

Description

display root edge

Usage

geom_rootedge(rootedge = NULL, ...)

Arguments

rootedge	length of rootedge; use phylo$root.edge if rootedge = NULL (by default).
...	additional parameters Additional parameters can be referred to the following parameters: size control the width of rootedge, default is 0.5. colour color of rootedge, default is black. linetype the type of line, default is 1. alpha modify colour transparency, default is 1.

Details

geom_rootedge is used to create a rootedge.

Value

ggtree rootedge layer

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

Examples

library(ggtree)
set.seed(123)
## with root edge = 1
tree1 <- read.tree(text='((A:1,B:2):3,C:2):1;')
ggtree(tree1) + geom_tiplab() + geom_rootedge()

## without root edge
tree2 <- read.tree(text='((A:1,B:2):3,C:2);')
ggtree(tree2) + geom_tiplab() + geom_rootedge()

## setting root edge
tree2$root.edge <- 2
ggtree(tree2) + geom_tiplab() + geom_rootedge()

## specify length of root edge for just plotting
## this will ignore tree$root.edge
ggtree(tree2) + geom_tiplab() + geom_rootedge(rootedge = 3)

## For more information about tree visualization, please refer to the online book
## https://yulab-smu.top/treedata-book/chapter4.html

ggtree documentation built on Nov. 15, 2020, 2:09 a.m.