geom_rootedge: geom_rootedge

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

geom_rootedge

Description

display root edge layer for a tree

Usage

geom_rootedge(rootedge = NULL, ...)

Arguments

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

Details

geom_rootedge is used to create a rootedge as ggtree doesn’t plot the root edge by default.

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 detailed demonstration of this function, please refer to chapter A.4.5 of 
## *Data Integration, Manipulation and Visualization of Phylogenetic Trees*
## <http://yulab-smu.top/treedata-book/index.html> by Guangchuang Yu.

YuLab-SMU/ggtree documentation built on April 15, 2024, 5:19 p.m.