hierarchical clustering on correlations in Python scipy/numpy?

Question

How can I run hierarchical clustering on a correlation matrix in scipy/numpy? I have a matrix of 100 rows by 9 columns, and I\'d like to hierarchicall

Answer 1

Just change the metric to correlation so that the first line becomes:

Y=pdist(X, 'correlation')

However, I believe that the code can be simplified to just:

Z=linkage(X, 'single', 'correlation')
dendrogram(Z, color_threshold=0)

because linkage will take care of the pdist for you.