Plot Hierarchical Clustering Dendrogram

This example plots the corresponding dendrogram of a hierarchical clustering using AgglomerativeClustering and the dendrogram method available in scipy.

Hierarchical Clustering Dendrogram
import numpy as np

from matplotlib import pyplot as plt
from scipy.cluster.hierarchy import dendrogram
from sklearn.datasets import load_iris
from sklearn.cluster import AgglomerativeClustering

def plot_dendrogram(model, **kwargs):
    # Create linkage matrix and then plot the dendrogram

    # create the counts of samples under each node
    counts = np.zeros(model.children_.shape[0])
    n_samples = len(model.labels_)
    for i, merge in enumerate(model.children_):
        current_count = 0
        for child_idx in merge:
            if child_idx < n_samples:
                current_count += 1  # leaf node
                current_count += counts[child_idx - n_samples]
        counts[i] = current_count

    linkage_matrix = np.column_stack([model.children_, model.distances_,

    # Plot the corresponding dendrogram
    dendrogram(linkage_matrix, **kwargs)

iris = load_iris()
X =

# setting distance_threshold=0 ensures we compute the full tree.
model = AgglomerativeClustering(distance_threshold=0, n_clusters=None)

model =
plt.title('Hierarchical Clustering Dendrogram')
# plot the top three levels of the dendrogram
plot_dendrogram(model, truncate_mode='level', p=3)
plt.xlabel("Number of points in node (or index of point if no parenthesis).")

Total running time of the script: ( 0 minutes 0.146 seconds)

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