utils.py 文件源码

def hierarch_cluster(M):
    """Cluster matrix using hierarchical clustering.

    Parameters
    ----------
    M : np.ndarray
        Matrix, for example, distance matrix.

    Returns
    -------
    Mclus : np.ndarray
        Clustered matrix.
    indices : np.ndarray
        Indices used to cluster the matrix.
    """
    import scipy as sp
    import scipy.cluster
    link = sp.cluster.hierarchy.linkage(M)
    indices = sp.cluster.hierarchy.leaves_list(link)
    Mclus = np.array(M[:, indices])
    Mclus = Mclus[indices, :]
    if False:
        pl.matshow(Mclus)
        pl.colorbar()
    return Mclus, indices