plot_phylo: Plot a 'phylo' tree object

In StoreyLab/popkin: Estimate Kinship and FST under Arbitrary Population Structure

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,
  edge_width = 1,
  ...
)

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).
edge_width	The width of the tree edges (passed to ape::plot.phylo() as edge.width).
...	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)).

See Also

plot_popkin() can create multipanel figures including kinship matrices and trees (calling the present function in the process).

Examples

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

# plot it!
plot_phylo( tree )

StoreyLab/popkin documentation built on Jan. 10, 2023, 1:39 p.m.