Change which axis is used as radial/angular position with matplotlib polar=True (Creating circular phylogenetic tree with Bio.Phylo)

Question

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?

did you try tree.ladderize() before Phylo.draw(tree) as per https://biopython.org/wiki/Phylo — pippo1980, Mar 21 '23 at 17:33
phylo.draw is here: https://github.com/biopython/biopython/blob/master/Bio/Phylo/_utils.py#L180 — pippo1980, Mar 21 '23 at 17:42
@pippo1980 I know these, but I still don't know the answer. I suppose that one of the keyword arguments might do the trick... — Roger Vadim, Mar 21 '23 at 17:53
not really more circular that the standard ouput, didnt have a look at the OP requset https://i.stack.imgur.com/NCPhu.png — pippo1980, Mar 21 '23 at 17:59
@RogerVadim FYI I have added a solution if you are still interested in one for this question — John Collins, Sep 02 '23 at 06:47
@JohnCollins thank you. It is not of immediate importance now, but I am still interested in your solution. — Roger Vadim, Sep 02 '23 at 11:36

John Collins · Accepted Answer · 2023-09-01T19:57:18.380

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.

^{Further detailing work could be done to mimic plotting portions of the circumference of the polar circle (i.e., arcs) at branch points, as would typically be seen in a radial phylogenetic map. Also, as it is, the transformation performed here on the coordinates does not seem to do well at extending perfectly balanced within and throughout the circle.}

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-").}

Change which axis is used as radial/angular position with matplotlib polar=True (Creating circular phylogenetic tree with Bio.Phylo)

1 Answers1

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

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