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SciPy Reference Guide, Release 0.8.dev Indices k < n correspond to original observations while indices k ≥ n correspond to non-singleton clusters. For example, to label singletons with their node id and non-singletons with their id, count, and inconsistency coefficient, simply do: # First define the leaf label function. def llf(id): if id < n: return str(id) else: return ’[%d %d %1.2f]’ % (id, count, R[n-id,3]) # The text for the leaf nodes is going to be big so force # a rotation of 90 degrees. dendrogram(Z, leaf_label_func=llf, leaf_rotation=90) • show_contracted : bool When True the heights of non-singleton nodes contracted into a leaf node are plotted as crosses along the link connecting that leaf node. This really is only useful when truncation is used (see truncate_mode parameter). • link_color_func : lambda/function When a callable function, link_color_function is called with each non-singleton id corresponding to each U-shaped link it will paint. The function is expected to return the color to paint the link, encoded as a matplotlib color string code. For example: dendrogram(Z, link_color_func=lambda k: colors[k]) colors the direct links below each untruncated non-singleton node k using colors[k]. Returns • R : dict A dictionary of data structures computed to render the dendrogram. Its has the following keys: – ‘icoords’: a list of lists [I1, I2, ..., Ip] where Ik is a list of 4 independent variable coordinates corresponding to the line that represents the k’th link painted. – ‘dcoords’: a list of lists [I2, I2, ..., Ip] where Ik is a list of 4 independent variable coordinates corresponding to the line that represents the k’th link painted. – ‘ivl’: a list of labels corresponding to the leaf nodes. – ‘leaves’: for each i, H[i] == j, cluster node j appears in the i th position in the left-to-right traversal of the leaves, where j < 2n − 1 and i < n. If j is less than n, the i th leaf node corresponds to an original observation. Otherwise, it corresponds to a non-singleton cluster. fcluster(Z, t, criterion=’inconsistent’, depth=2, R=None, monocrit=None) Forms flat clusters from the hierarchical clustering defined by the linkage matrix Z. The threshold t is a required parameter. Arguments 136 Chapter 3. Reference
Returns SciPy Reference Guide, Release 0.8.dev • Z : ndarray The hierarchical clustering encoded with the matrix returned by the linkage function. • t : double The threshold to apply when forming flat clusters. • criterion : string (optional) The criterion to use in forming flat clusters. This can be any of the following values: – ‘inconsistent’: If a cluster node and all its decendents have an inconsistent value less than or equal to t then all its leaf descendents belong to the same flat cluster. When no non-singleton cluster meets this criterion, every node is assigned to its own cluster. (Default) – ‘distance’: Forms flat clusters so that the original observations in each flat cluster have no greater a cophenetic distance than t. – ‘maxclust’: Finds a minimum threshold r so that the cophenetic distance between any two original observations in the same flat cluster is no more than r and no more than t flat clusters are formed. – ‘monocrit’: Forms a flat cluster from a cluster node c with index i when monocrit[j]
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