55 lines
1.7 KiB
Python
55 lines
1.7 KiB
Python
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# Authors: Mathew Kallada, Andreas Mueller
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# License: BSD 3 clause
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"""
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=========================================
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Plot Hierarchical Clustering Dendrogram
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=========================================
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This example plots the corresponding dendrogram of a hierarchical clustering
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using AgglomerativeClustering and the dendrogram method available in scipy.
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"""
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import numpy as np
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from matplotlib import pyplot as plt
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from scipy.cluster.hierarchy import dendrogram
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from sklearn.cluster import AgglomerativeClustering
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from sklearn.datasets import load_iris
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def plot_dendrogram(model, **kwargs):
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# Create linkage matrix and then plot the dendrogram
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# create the counts of samples under each node
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counts = np.zeros(model.children_.shape[0])
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n_samples = len(model.labels_)
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for i, merge in enumerate(model.children_):
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current_count = 0
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for child_idx in merge:
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if child_idx < n_samples:
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current_count += 1 # leaf node
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else:
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current_count += counts[child_idx - n_samples]
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counts[i] = current_count
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linkage_matrix = np.column_stack(
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[model.children_, model.distances_, counts]
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).astype(float)
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# Plot the corresponding dendrogram
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dendrogram(linkage_matrix, **kwargs)
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iris = load_iris()
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X = iris.data
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# setting distance_threshold=0 ensures we compute the full tree.
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model = AgglomerativeClustering(distance_threshold=0, n_clusters=None)
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model = model.fit(X)
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plt.title("Hierarchical Clustering Dendrogram")
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# plot the top three levels of the dendrogram
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plot_dendrogram(model, truncate_mode="level", p=3)
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plt.xlabel("Number of points in node (or index of point if no parenthesis).")
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plt.show()
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