Extract rows of clusters in hierarchical clustering using seaborn clustermap

Question

I am using hierarchical clustering from seaborn.clustermap to cluster my data. This works fine to nicely visualize the clusters in a heatmap. However, now I would like to extract all row values that are assigned to the different clusters.

This is what my data looks like:

import pandas as pd

# load DataFrame 
df = pd.read_csv('expression_data.txt', sep='\t', index_col=0)

df

    log_HU1         log_HU2
EEF1A1  13.439499   13.746856
HSPA8   13.169191   12.983910
FTH1    13.861164   13.511200
PABPC1  12.142340   11.885885
TFRC    11.261368   10.433607
RPL26   13.837205   13.934710
NPM1    12.381585   11.956855
RPS4X   13.359880   12.588574
EEF2    11.076926   11.379336
RPS11   13.212654   13.915813
RPS2    12.910164   13.009184
RPL11   13.498649   13.453234
CA1 9.060244    13.152061
RPS3    11.243343   11.431791
YBX1    12.135316   12.100374
ACTB    11.592359   12.108637
RPL4    12.168588   12.184330
HSP90AA1    10.776370   10.550427
HSP90AB1    11.200892   11.457365
NCL 11.366145   11.060236

Then I perform the clustering using seaborn as follows:

fig = sns.clustermap(df)

Which produces the following clustermap:

For this example I may be able to manually interpret the values belonging to each cluster (e.g. that TFRC and HSP90AA1 cluster). However I am planning to do these clustering analysis on much bigger data sets.

So my question is: does anyone know how to get the row values belonging to each cluster?

Thanks,

this was ansered here: stackoverflow.com/questions/27924813/… — Mateo Torres
Possible duplicate of Extracting clusters from seaborn clustermap — Mateo Torres
Yeah, I tried that one. But I definitely don't get it to work. So if you know how to? I would be really thankful! — pr94
Have you tried fcluster? as suggested here: stackoverflow.com/a/16023123/943138 (this will also require you to compute the linkage outside of seaborn's clustermap) — Mateo Torres

pr94 pr94 · Accepted Answer · 2019-12-29T08:24:52

Using scipy.cluster.hierarchy module with fcluster allows cluster retrieval:

import pandas as pd
import seaborn as sns
import scipy.cluster.hierarchy as sch

df = pd.read_csv('expression_data.txt', sep='\t', index_col=0)

# retrieve clusters using fcluster 
d = sch.distance.pdist(df)
L = sch.linkage(d, method='complete')
# 0.2 can be modified to retrieve more stringent or relaxed clusters
clusters = sch.fcluster(L, 0.2*d.max(), 'distance')

# clusters indicices correspond to incides of original df
for i,cluster in enumerate(clusters):
    print(df.index[i], cluster)

Out:

EEF1A1 2
HSPA8 1
FTH1 2
PABPC1 3
TFRC 5
RPL26 2
NPM1 3
RPS4X 1
EEF2 4
RPS11 2
RPS2 1
RPL11 2
CA1 6
RPS3 4
YBX1 3
ACTB 3
RPL4 3
HSP90AA1 5
HSP90AB1 4
NCL 4

Extract rows of clusters in hierarchical clustering using seaborn clustermap

1 Answers