scipy linkage format

python scipy dendrogram
geo_pythoncl picture geo_pythoncl · Mar 23, 2012 · Viewed 28.6k times · Source

I have written my own clustering routine and would like to produce a dendrogram. The easiest way to do this would be to use scipy dendrogram function. However, this requires the input to be in the same format that the scipy linkage function produces. I cannot find an example of how the output of this is formatted. I was wondering whether someone out there can enlighten me.

Answer

dkar picture dkar · Jun 8, 2012

This is from the scipy.cluster.hierarchy.linkage() function documentation, I think it's a pretty clear description for the output format:

A (n-1) by 4 matrix Z is returned. At the i-th iteration, clusters with indices Z[i, 0] and Z[i, 1] are combined to form cluster n + i. A cluster with an index less than n corresponds to one of the original observations. The distance between clusters Z[i, 0] and Z[i, 1] is given by Z[i, 2]. The fourth value Z[i, 3] represents the number of original observations in the newly formed cluster.

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