Dendrogram

Polar Phylogenetic Tree Dark

Real polar dendrogram for phylogenetic analysis with proper scipy transformation

Output
Polar Phylogenetic Tree Dark
Python
import matplotlib.pyplot as plt
import numpy as np
from scipy.cluster.hierarchy import dendrogram, linkage, set_link_color_palette

np.random.seed(123)

species = ['Human', 'Chimp', 'Gorilla', 'Orangutan', 'Macaque', 'Mouse', 
           'Rat', 'Dog', 'Cat', 'Cow', 'Pig', 'Horse']
n = len(species)
genetic_data = np.random.rand(n, 6) * 50
Z = linkage(genetic_data, method='average')

fig_temp, ax_temp = plt.subplots()
set_link_color_palette(['#27D3F5', '#F5276C', '#6CF527', '#F5B027', '#5314E6'])
dn = dendrogram(Z, labels=species, no_plot=False, color_threshold=0.6*max(Z[:,2]),
                above_threshold_color='#666666', ax=ax_temp)
plt.close(fig_temp)

icoord = np.array(dn['icoord'])
dcoord = np.array(dn['dcoord'])
colors = dn['color_list']

x_min, x_max = icoord.min(), icoord.max()
y_max = dcoord.max()

def to_polar(x, y):
    theta = (x - x_min) / (x_max - x_min) * 2 * np.pi * 0.92 + np.pi * 0.04
    r = y / y_max * 0.65 + 0.3
    return theta, r

fig, ax = plt.subplots(figsize=(10, 10), subplot_kw={'projection': 'polar'}, facecolor='#0a0a0f')
ax.set_facecolor('#0a0a0f')

for ic, dc, color in zip(icoord, dcoord, colors):
    thetas, rs = [], []
    for x, y in zip(ic, dc):
        t, r = to_polar(x, y)
        thetas.append(t)
        rs.append(r)
    
    # Glow effect
    for lw, alpha in [(4, 0.15), (2, 0.9)]:
        ax.plot([thetas[0], thetas[1]], [rs[0], rs[1]], color=color, linewidth=lw, alpha=alpha)
        ax.plot([thetas[2], thetas[3]], [rs[2], rs[3]], color=color, linewidth=lw, alpha=alpha)
        if thetas[1] != thetas[2]:
            arc_thetas = np.linspace(min(thetas[1], thetas[2]), max(thetas[1], thetas[2]), 40)
            ax.plot(arc_thetas, [rs[1]]*len(arc_thetas), color=color, linewidth=lw, alpha=alpha)

leaf_positions = np.linspace(x_min, x_max, n)
for i, (pos, label) in enumerate(zip(leaf_positions, dn['ivl'])):
    theta, _ = to_polar(pos, 0)
    rotation = np.degrees(theta) - 90 if np.pi/2 < theta < 3*np.pi/2 else np.degrees(theta) + 90
    ha = 'right' if np.pi/2 < theta < 3*np.pi/2 else 'left'
    ax.text(theta, 0.2, label, ha=ha, va='center', fontsize=9, color='#27D3F5',
            rotation=rotation, rotation_mode='anchor', fontweight='500')
    
    color = ['#27D3F5', '#F5276C', '#6CF527', '#F5B027', '#5314E6'][i % 5]
    ax.scatter(theta, 0.3, c=color, s=50, zorder=5, edgecolor='white', linewidth=0.5)

ax.set_ylim(0, 1.05)
ax.set_yticklabels([])
ax.set_xticklabels([])
ax.spines['polar'].set_visible(False)
ax.grid(True, color='#1a1a3f', alpha=0.4)

ax.set_title('Phylogenetic Circular Tree', fontsize=14, color='white', fontweight='bold', y=1.08)

plt.tight_layout()
plt.show()
Library

Matplotlib

Category

Statistical

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