weighted#
- scipy.cluster.hierarchy.weighted(y)[source]#
- Perform weighted/WPGMA linkage on the condensed distance matrix. - See - linkagefor more information on the return structure and algorithm.- Parameters:
- yndarray
- The upper triangular of the distance matrix. The result of - pdistis returned in this form.
 
- Returns:
- Zndarray
- A linkage matrix containing the hierarchical clustering. See - linkagefor more information on its structure.
 
 - See also - linkage
- for advanced creation of hierarchical clusterings. 
- scipy.spatial.distance.pdist
- pairwise distance metrics 
 - Examples - >>> from scipy.cluster.hierarchy import weighted, fcluster >>> from scipy.spatial.distance import pdist - First, we need a toy dataset to play with: - x x x x x x x x x x x x - >>> X = [[0, 0], [0, 1], [1, 0], ... [0, 4], [0, 3], [1, 4], ... [4, 0], [3, 0], [4, 1], ... [4, 4], [3, 4], [4, 3]] - Then, we get a condensed distance matrix from this dataset: - >>> y = pdist(X) - Finally, we can perform the clustering: - >>> Z = weighted(y) >>> Z array([[ 0. , 1. , 1. , 2. ], [ 6. , 7. , 1. , 2. ], [ 3. , 4. , 1. , 2. ], [ 9. , 11. , 1. , 2. ], [ 2. , 12. , 1.20710678, 3. ], [ 8. , 13. , 1.20710678, 3. ], [ 5. , 14. , 1.20710678, 3. ], [10. , 15. , 1.20710678, 3. ], [18. , 19. , 3.05595762, 6. ], [16. , 17. , 3.32379407, 6. ], [20. , 21. , 4.06357713, 12. ]]) - The linkage matrix - Zrepresents a dendrogram - see- scipy.cluster.hierarchy.linkagefor a detailed explanation of its contents.- We can use - scipy.cluster.hierarchy.fclusterto see to which cluster each initial point would belong given a distance threshold:- >>> fcluster(Z, 0.9, criterion='distance') array([ 7, 8, 9, 1, 2, 3, 10, 11, 12, 4, 6, 5], dtype=int32) >>> fcluster(Z, 1.5, criterion='distance') array([3, 3, 3, 1, 1, 1, 4, 4, 4, 2, 2, 2], dtype=int32) >>> fcluster(Z, 4, criterion='distance') array([2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 1], dtype=int32) >>> fcluster(Z, 6, criterion='distance') array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], dtype=int32) - Also, - scipy.cluster.hierarchy.dendrogramcan be used to generate a plot of the dendrogram.