silhouette.py 文件源码

def single_silhouette_dendrogram(dist_matrix, Z, threshold, mode='clusters',
                                 method='single', sample_names=None):
    """Compute the average silhouette at a given threshold.

    Parameters
    ----------
    dist_matrix : array-like
        Precomputed distance matrix between points.
    Z : array-like
        Linkage matrix, results of scipy.cluster.hierarchy.linkage.
    threshold : float
        Specifies where to cut the dendrogram.
    mode : ('clusters', 'thresholds'), optional
        Choose what to visualise on the x-axis.

    Returns
    -------
    x : float
        Based on mode, it can contains the number of clusters or threshold.
    silhouette_avg : float
        The average silhouette.
    """
    cluster_labels = fcluster(Z, threshold, 'distance')
    nclusts = np.unique(cluster_labels).shape[0]

    save_results_clusters("res_{}_{:03d}_clust.csv".format(method, nclusts),
                          sample_names, cluster_labels)

    try:
        silhouette_list = silhouette_samples(dist_matrix, cluster_labels,
                                             metric="precomputed")
        silhouette_avg = np.mean(silhouette_list)
        x = max(cluster_labels) if mode == 'clusters' else threshold
    except ValueError as e:
        if max(cluster_labels) == 1:
            x = 1 if mode == 'clusters' else threshold
            silhouette_avg = 0
        else:
            raise(e)

    return x, silhouette_avg