python distance matrix_python hcluster，距离矩阵和压缩距离矩阵 (python hcluster, distance matrix and condensed d...

I knocked up a quick random example similar to yours and experienced the same problem.

In the docstring it does say :

Performs hierarchical/agglomerative clustering on the

condensed distance matrix y. y must be a :math:{n \choose 2} sized

vector where n is the number of original observations paired

in the distance matrix.

However, having had a quick look at the code, it seems like the intent is for it to both work with vector shaped and matrix shaped code:

In hierachy.py there is a switch based upon the shape of the matrix.

It seems however that the key bit of info is in the function linkage's docstring:

- Q : ndarray

A condensed or redundant distance matrix. A condensed

distance matrix is a flat array containing the upper

triangular of the distance matrix. This is the form that

``pdist`` returns. Alternatively, a collection of

:math:`m` observation vectors in n dimensions may be passed as

a :math:`m` by :math:`n` array.

So I think that the interface doesn't allow the passing of a distance matrix.

Instead it thinks you are passing it m observation vectors in n dimensions .

Hence the difference in result?

Does that seem reasonable?

Else just take a look at the code itself I'm sure you'll be able to debug it and figure out why your examples are different.

Cheers

Matt