Biopython tree

This example shows how to use iplotx to plot trees from Biopython’s Phylo module.

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

# Make a tree from a string in Newick format
tree = next(
    Phylo.NewickIO.parse(
        StringIO(
            "(()(()((()())(()()))))",
        )
    )
)

ipx.plotting.tree(
    tree,
)

<iplotx.tree.TreeArtist object at 0x7af382c1f610>

To add labels to the leaves, you can use the leaf_labels argument as a dictionary. Moreover, the plot can be customised further using hmargin (horizontal label margin) and some matplotlib settings.

# sphinx_gallery_thumbnail_number = 2
leaf_labels = {leaf: f"Species {i + 1}" for i, leaf in enumerate(tree.get_terminals())}
fig, ax = plt.subplots(figsize=(4, 4))
ipx.plotting.tree(
    tree,
    ax=ax,
    leaf_labels=leaf_labels,
    leaf_label_hmargin=10,
    leaf_deep=False,
)
ax.set_xlim(0, 8)
ax.invert_yaxis()

iplotx can compute a radial tree layout as well, and usual style modifications work for trees same as networks:

ipx.plotting.tree(
    tree,
    layout="radial",
    style=[
        "tree",
        {
            "edge": {
                "color": ["black", "pink"],
                "linewidth": 4,
            },
        },
    ],
    aspect=1,
    title="Black pink in your area",
)

<iplotx.tree.TreeArtist object at 0x7af382c30e10>