popkin: plot_phylo – R documentation

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plot_phylo

Plot a phylo tree object

Description

This is a wrapper around ape::plot.phylo() that makes several adjustments so plots agree more with accompanying kinship matrices. In particular, tree is reversed on the y-axis to match matrix orientation, y-axis spacing is more padded for small trees, and an x-axis scale is always added.

Usage

plot_phylo(tree, xlab = "Coancestry", xmax = NULL, leg_n = 5, ...)

Arguments

`tree`	A `phylo` object to plot.
`xlab`	The x-axis label (default "Coancestry").
`xmax`	X-axis maximum limit.
`leg_n`	The desired number of ticks in the x-axis (input to `pretty()`, see that for more details).
`...`	Additional parameters passed to `ape::plot.phylo()`. However, these parameters cannot be passed: `x.lim` (controlled via `xmax`), `y.lim` (a better default for small trees is passed and cannot be changed) and `font` (takes the value of `par('font')` instead of `ape`'s default of 3 (italic)).

Examples

# create a small random tree
library(ape)
tree <- rtree( 3 )

# plot it!
plot_phylo( tree )

popkin

Estimate Kinship and FST under Arbitrary Population Structure

v1.3.13

GPL-3

Authors

Alejandro Ochoa [aut, cre] (<https://orcid.org/0000-0003-4928-3403>), John D. Storey [aut] (<https://orcid.org/0000-0001-5992-402X>)

Initial release