Dendrogram

Complete Linkage Radial Dark

Complete linkage hierarchical clustering in circular layout

Output
Complete Linkage Radial 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(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='#444444', 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='#0a0a0f')
ax.set_facecolor('#0a0a0f')

# Inner circle fill
circle_theta = np.linspace(0, 2*np.pi, 100)
ax.fill(circle_theta, [0.42]*100, color='#1a1a2e', alpha=0.5)

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='white',
            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='white', linewidth=0.5)

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='white', fontweight='bold', y=1.08)

plt.tight_layout()
plt.show()
Library

Matplotlib

Category

Statistical

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