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,
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
Run this code# create a small random tree
library(ape)
tree <- rtree( 3 )
# plot it!
plot_phylo( tree )
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