Extracting clusters from seaborn clustermap

Question

I am using the seaborn clustermap to create clusters and visually it works great (this example produces very similar results).

However I am having troub

Answer 1

You probably want a new column in your dataframe with the cluster membership. I've managed to do this from assembled snippets of code stolen from all over the web:

import seaborn
import scipy

g = seaborn.clustermap(df,method='average')
den = scipy.cluster.hierarchy.dendrogram(g.dendrogram_col.linkage,
                                         labels = df.index,
                                         color_threshold=0.60)  
from collections import defaultdict

def get_cluster_classes(den, label='ivl'):
    cluster_idxs = defaultdict(list)
    for c, pi in zip(den['color_list'], den['icoord']):
        for leg in pi[1:3]:
            i = (leg - 5.0) / 10.0
            if abs(i - int(i)) < 1e-5:
                cluster_idxs[c].append(int(i))

    cluster_classes = {}
    for c, l in cluster_idxs.items():
        i_l = [den[label][i] for i in l]
        cluster_classes[c] = i_l

    return cluster_classes

clusters = get_cluster_classes(den)

cluster = []
for i in df.index:
    included=False
    for j in clusters.keys():
        if i in clusters[j]:
            cluster.append(j)
            included=True
    if not included:
        cluster.append(None)

df["cluster"] = cluster

So this gives you a column with 'g' or 'r' for the green- or red-labeled clusters. I determine my color_threshold by plotting the dendrogram, and eyeballing the y-axis values.

Answer 2

While using result.linkage.dendrogram_col or result.linkage.dendrogram_row will currently work, it seems to be an implementation detail. The safest route is to first compute the linkages explicitly and pass them to the clustermap function, which has row_linkage and col_linkage parameters just for that.

Replacing the last line in your example (result = ...) with the following code gives the same result as before, but you will also have row_linkage and col_linkage variables that you can use with fcluster etc.

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

correlations = df.corr()
correlations_array = np.asarray(df.corr())

row_linkage = hierarchy.linkage(
    distance.pdist(correlations_array), method='average')

col_linkage = hierarchy.linkage(
    distance.pdist(correlations_array.T), method='average')

sns.clustermap(correlations, row_linkage=row_linkage, col_linkage=col_linkage, row_colors=network_colors, method="average",
               col_colors=network_colors, figsize=(13, 13), cmap=cmap)

In this particular example, the code could be simplified more since the correlations array is symmetric and therefore row_linkage and col_linkage will be identical.

Note: A previous answer included a call to distance.squareshape according to what the code in seaborn does, but that is a bug.