Angular layout and edge waypoints

This example demonstrates iplotx’s capability to style tree appearance with an angular look, either for the whole tree or specific edges.

Tip

“Waypoints” and “angular” are opposites. When an edge uses waypoints, you can say it is using an angular style.

from Bio import Phylo
from io import StringIO
import matplotlib.pyplot as plt
import iplotx as ipx

tree = Phylo.read(
    StringIO("(((A,B),(C,D)),(E,F,G));"),
    format="newick",
)

fig, axs = plt.subplots(2, 2, figsize=(9, 9))
ipx.tree(
    tree,
    ax=axs[0, 0],
    title="Default\n(with waypoints)",
)
ipx.tree(
    tree,
    ax=axs[0, 1],
    layout_angular=True,
    title="Angular",
)
ipx.tree(
    tree,
    ax=axs[1, 0],
    edge_waypoints=False,
    title="Angular\n(via edge_waypoints)",
)
ipx.tree(
    tree,
    ax=axs[1, 1],
    edge_waypoints=[True, False],
    title="Mixed",
)

<iplotx.tree.TreeArtist object at 0x7af382c96490>

Warning

For waypoints, None and the string "none" are interpreted differently by iplotx. The latter "none" means no waypoints, whereas the Python singleton None means letting iplotx determine the correct type of waypoints. None is equivalent to True, while "none" is equivalent to False.

You can even specify angularity on a per-edge basis with a defaultdict:

from collections import defaultdict

ipx.tree(
    tree,
    edge_waypoints=defaultdict(lambda: True, {tree.clade[0, 1]: False}),
    title="Mixed\n(per-edge)",
)

<iplotx.tree.TreeArtist object at 0x7af390d92490>

Note

iplotx’s fallback for per-element styling is the constructor for the type used by the first value of the dictionary, in this case bool() which returns False. Therefore, if we are ok with angular edges as the fallback, we can skip the defaultdict altogether:

ipx.tree(
    tree,
    edge_waypoints={tree.clade[0, 1]: True},
    title="Mixed per-edge\n(default fallback)",
)

<iplotx.tree.TreeArtist object at 0x7af390d01d10>

You can also mix booleans and other types, although it is not very readable:

ipx.tree(
    tree,
    edge_waypoints=[True, "none"],
    title="Mixed",
)

<iplotx.tree.TreeArtist object at 0x7af3901dd590>