Dendrogram

Complete Linkage Radial Light

Light theme complete linkage in circular dendrogram layout

Output
Complete Linkage Radial Light
Python
import matplotlib.pyplot as plt
import numpy as np
from scipy.cluster.hierarchy import dendrogram, linkage, set_link_color_palette

np.random.seed(987)

n = 20
labels = [f'C{i}' for i in range(1, n+1)]
data = np.random.rand(n, 5) * 70
Z = linkage(data, method='complete')

fig_temp, ax_temp = plt.subplots()
set_link_color_palette(['#6CF527', '#F5276C', '#27D3F5', '#F5B027', '#5314E6'])
dn = dendrogram(Z, labels=labels, no_plot=False, color_threshold=0.65*max(Z[:,2]),
                above_threshold_color='#9ca3af', 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 * 0.94 + np.pi * 0.03
    r = y / y_max * 0.5 + 0.45
    return theta, r

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

# Inner circle fill
circle_theta = np.linspace(0, 2*np.pi, 100)
ax.fill(circle_theta, [0.42]*100, color='#f9fafb', alpha=0.8)

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)
    
    ax.plot([thetas[0], thetas[1]], [rs[0], rs[1]], color=color, linewidth=2.5, alpha=0.9)
    ax.plot([thetas[2], thetas[3]], [rs[2], rs[3]], color=color, linewidth=2.5, alpha=0.9)
    if thetas[1] != thetas[2]:
        arc_thetas = np.linspace(min(thetas[1], thetas[2]), max(thetas[1], thetas[2]), 50)
        ax.plot(arc_thetas, [rs[1]]*len(arc_thetas), color=color, linewidth=2.5, alpha=0.9)

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, 0.32, label, ha=ha, va='center', fontsize=8, color='#374151',
            rotation=rotation, rotation_mode='anchor')
    
    color = ['#6CF527', '#F5276C', '#27D3F5', '#F5B027', '#5314E6'][i % 5]
    ax.scatter(theta, 0.45, c=color, s=45, zorder=5, edgecolor='#ffffff', linewidth=0.8)

ax.set_ylim(0, 1.02)
ax.set_yticklabels([])
ax.set_xticklabels([])
ax.spines['polar'].set_visible(False)
ax.grid(False)

ax.set_title('Complete Linkage - Circular View', fontsize=14, color='#1f2937', fontweight='bold', y=1.08)

plt.tight_layout()
plt.show()
Library

Matplotlib

Category

Statistical

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