CODEWITHSUNDEEP
pythonscipycluster-analysishierarchical-clustering
Nilani Algiriyage
Nilani Algiriyage

Reputation: 35696

How to get non-singleton cluster ids in scipy hierachical clustering

According to this we can get labels for non-singleton clusters.

I tried this with a simple example.

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

mat = np.array([[ 0. , 1. , 3.  ,0. ,2.  ,3.  ,1.],
 [ 1. , 0. , 3. , 1.,  1. , 2. , 2.],
 [ 3.,  3. , 0.,  3. , 3.,  3. , 4.],
 [ 0. , 1. , 3.,  0. , 2. , 3.,  1.],
 [ 2. , 1.,  3. , 2.,  0. , 1.,  3.],
 [ 3. , 2.,  3. , 3. , 1. , 0. , 3.],
 [ 1. , 2.,  4. , 1. , 3.,  3. , 0.]])

def llf(id):
    if id < n:
        return str(id)
    else:
        return '[%d %d %1.2f]' % (id, count, R[n-id,3])


linkage_matrix = linkage(mat, "complete")

dendrogram(linkage_matrix,
           p=4,
           leaf_label_func=llf,
           color_threshold=1,
           truncate_mode='lastp',
           distance_sort='ascending')

plt.show()

What are n, and count here?In a diagram like following I need to know who are listed under(3) and (2)?enter image description here

Upvotes: 0

Views: 1059

Answers (1)

CT Zhu
CT Zhu

Reputation: 54340

I think the document is not very clear at this part and the sample code in it is not even operational. But it is clear that 1 means the 2nd observation and (3) means there are 3 observation in that node.

If you want to know what are the 3 obs. in the 2nd node, if that is your question:

In [51]:
D4=dendrogram(linkage_matrix,
              color_threshold=1,
              p=4,
              truncate_mode='lastp',
              distance_sort='ascending')
D7=dendrogram(linkage_matrix,
              color_list=['g',]*7,
              p=7,
              truncate_mode='lastp',
              distance_sort='ascending', no_plot=True)  
from itertools import groupby
[list(group) for key, group in groupby(D7['ivl'],lambda x: x in D4['ivl'])]
Out[51]:
[['1'], ['6', '0', '3'], ['2'], ['4', '5']]

The 2nd node contains obs. 7th, 1th and 4th, and the 2th node contains the 5th and the 6th observations.

Upvotes: 1

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