pyckmeans.ordering package
Module contents
Module for distance matrix ordering.
- exception pyckmeans.ordering.InvalidLinkageType
Bases:
Exception
- exception pyckmeans.ordering.InvalidReorderMethod
Bases:
Exception
- pyckmeans.ordering.condensed_form(dist: numpy.ndarray) numpy.ndarray
Convert n*n distance matrix to condensed vector form.
- Parameters
- distnumpy.ndarray
n * n distance matrix.
- Returns
- numpy.ndarray
Distance matrix in condensed vector form as expected by scipy.cluster.hierarchy.linkage.
- pyckmeans.ordering.distance_order(dist: Union[numpy.ndarray, pyckmeans.distance.DistanceMatrix], method: str = 'GW', linkage_type: str = 'average') numpy.ndarray
Get optimal distance matrix order.
- Parameters
- distUnion[numpy.ndarray, ‘pyckmeans.distance.DistanceMatrix’]
A n * n distance matrix as either numpy.ndarray or as pyckmeans.distance.DistanceMatrix object.
- methodstr
Reordering method. Either ‘GW’ (Gruvaeus & Wainer, 1972) or ‘OLO’ for scipy.hierarchy.optimal_leaf_ordering.
Gruvaeus, G., H., Wainer. 1972. Two Additions to Hierarchical Cluster Analysis. The British Psychological Society 25.
- linkage_typestr
Linkage type for the hierarchical clustering. One of
‘average’
‘complete’
‘single’
‘weighted’
‘centroid’
See scipy.cluster.hierarchy.linkage for details.
- Returns
- numpy.ndarray
Optimal order as vector.
- Raises
- InvalidReorderMethod
Raised if an unknown reordering method is passed.
- InvalidLinkageType
Raised if an unknown linakage type is passed.
- pyckmeans.ordering.reorder_distance(dist: Union[numpy.ndarray, pyckmeans.distance.DistanceMatrix], method: str = 'GW', linkage_type: str = 'average') Union[numpy.ndarray, pyckmeans.distance.DistanceMatrix]
Reorder distance matrix using hierarchical clustering.
- Parameters
- distUnion[numpy.ndarray, ‘pyckmeans.distance.DistanceMatrix’]
A n * n distance matrix as either numpy.ndarray or as pyckmeans.distance.DistanceMatrix object.
- methodstr
Reordering method. Either ‘GW’ (Gruvaeus & Wainer, 1972) or ‘OLO’ for scipy.hierarchy.optimal_leaf_ordering.
Gruvaeus, G., H., Wainer. 1972. Two Additions to Hierarchical Cluster Analysis. The British Psychological Society 25.
- linkage_typestr
Linkage type for the hierarchical clustering. One of
‘average’
‘complete’
‘single’
‘weighted’
‘centroid’
See scipy.cluster.hierarchy.linkage for details.
- Returns
- Union[numpy.ndarray, ‘pyckmeans.distance.DistanceMatrix’]
The sorted distance matrix as either numpy.ndarray or pyckmeans.distance.DistanceMatrix, depending on the input.
- Raises
- InvalidReorderMethod
Raised if an unknown reordering method is passed.
- InvalidLinkageType
Raised if an unknown linakage type is passed.
- pyckmeans.ordering.reorder_linkage_gw(linkage: numpy.ndarray, dist: numpy.ndarray) numpy.ndarray
Reorder linkage matrix using the algorithm described by Gruvaeus & Wainer (1972) [1].
- Parameters
- linkagenumpy.ndarray
Linkage matrix as returned from scipy.cluster.hierarchy.linkage.
- distnumpy.ndarray
n * n distance matrix.
- Returns
- numpy.ndarray
Reordered linkage matrix.
References
- 1
Gruvaeus, G., H., Wainer. 1972. Two Additions to Hierarchical Cluster Analysis. The British Psychological Society 25.