If I create a phylogenetic tree using Biopython Phylo module, it is oriented from left to right, e.g.:

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

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

fig, ax = plt.subplots(1, 1, figsize=(6, 6))
Phylo.draw(tree, axes=ax, do_show=False)
plt.savefig("./tree_rect.png")
plt.close(fig)

produces

If I now try to convert it to a circular tree using the built-in polar transformation of matplotlib, I obtain:

fig, ax = plt.subplots(subplot_kw=dict(polar=True), figsize=(6, 6))
Phylo.draw(tree, axes=ax, do_show=False)
plt.savefig("./tree_circ.png")
plt.close(fig)

I obtain

that is matplotlib takes y-axis as the radial axis and x-axis as the angle. This is the opposite of what I need for obtaining a correct layout, which I can do, e.g., using ete3:

from ete3 import Tree, TreeStyle
t = Tree("(((A,B),(C,D)),(E,F,G));")
circular_style = TreeStyle()
circular_style.mode = "c"
circular_style.scale = 20
t.render("tree_ete3.png", w=183, units="mm", tree_style=circular_style)

(How) could this be done using Bio.Phylo? I suppose the possibilities are

• Changing the layout in Phylo.draw, so that the tree is directed upwards
• telling matplotlib polar transformation to use x-axis as the radial vector and y-axis as the angle

but I don't know how to do either (and whether it can be done.)

Related question: Python: How to convert a phylogenetic tree into a circular format?

Here is an example swapping the "x" and "y" coordinates in a matplotlib polar plot so that a radial phylogenetic tree is correctly branched

Below, I show how varying a scaling parameter in the code ('Scale' → z) affects the resulting tree, and also provide for comparison the normal Bio.Phylo.draw(tree) version of the map.

import matplotlib.pyplot as plt
import numpy as np
from Bio import Phylo
from io import StringIO


def transform_coordinates(
    clade, r=0, theta=0, delta_theta=np.pi / 32, coordinates=None
):
    if coordinates is None:
        coordinates = {}

    coordinates[clade] = (r, theta)

    if clade.is_terminal():
        theta += delta_theta
    else:
        for child in clade:
            coordinates, theta = transform_coordinates(
                child, r + 1, theta, delta_theta, coordinates
            )

    return coordinates, theta


def plot_tree(tree, coordinates, scale=1):
    fig, ax = plt.subplots(subplot_kw=dict(polar=True), figsize=(6, 6))
    for clade in tree.find_clades():
        if not clade.is_terminal():
            for child in clade:
                x1, y1 = coordinates[clade]
                x2, y2 = coordinates[child]
                ax.plot([y1, y2], [x1, x2], "k-")
                if child.is_terminal():
                    # print(child.name, x2, y2, np.cos(x2), np.cos(y2))
                    shift_y = 0.2 if np.cos(y2) < 0 else 0.05
                    ax.annotate(
                        child.name, xy=(y2 * 1.02, x2 + shift_y), color="red"
                    )
                ax.grid("off")
                ax.patch.set_visible(False)
                ax.spines["polar"].set_visible(False)
                ax.xaxis.grid(False)
                ax.xaxis.set_visible(False)
                ax.yaxis.grid(False)
                ax.yaxis.set_visible(False)
    plt.title(f"Scale = {scale}\n")
    plt.show()


handle = StringIO("((((A,B),(X,Y,Z),(H,I,J))),(((C,L),(D,K)),(E,F,G)));")
tree = Phylo.read(handle, "newick")

for z in range(12, 36, 4):
    coordinates, _ = transform_coordinates(tree.clade, delta_theta=np.pi / z)
    plot_tree(tree, coordinates, scale=z)

_{Note: The swapping of x & y coordinates within plot_tree: ax.plot([y1, y2], [x1, x2], "k-").}