Network Graph from SciPy Hierarchical Clustering

[rohithth]

Hi,

Using SciPy Hierarchical Clustering how can we create the network graph?

from matplotlib import pyplot as plt from scipy.cluster.hierarchy import dendrogram, linkage import numpy as np

generate two clusters: a with 100 points, b with 50:

np.random.seed(4711) # for repeatability of this tutorial a = np.random.multivariate_normal([10, 0], [[3, 1], [1, 4]], size=[100,]) b = np.random.multivariate_normal([0, 20], [[3, 1], [1, 4]], size=[50,]) X = np.concatenate((a, b),) print X.shape # 150 samples with 2 dimensions plt.scatter(X[:,0], X[:,1]) plt.show()

generate the linkage matrix

Z = linkage(X, 'ward')

from scipy.cluster.hierarchy import cophenet from scipy.spatial.distance import pdist

c, coph_dists = cophenet(Z, pdist(X)) c

calculate full dendrogram

plt.figure(figsize=(25, 10)) plt.title('Hierarchical Clustering Dendrogram') plt.xlabel('sample index') plt.ylabel('distance') dendrogram( Z, leaf_rotation=90., # rotates the x axis labels leaf_font_size=8., # font size for the x axis labels ) plt.show()

Now how do we plot the network graph like yours instead of dendrogram? Kindly assist. Thank you!

[GuyAllard]

Hi,

I think that this question would be more suitable for the NetworkX or SciPy discussion groups.

I am closing this issue as not relevant to this project.