cassiopeia.data.compute_dissimilarity_map

cassiopeia.data.compute_dissimilarity_map(cm, C, dissimilarity_function, weights=None, missing_state_indicator=- 1)

Compute the dissimilarity between all samples

An optimized function for computing pairwise dissimilarities between samples in a character matrix according to the dissimilarity function.

Parameters

cm : arrayarray

Character matrix

C : intint

Number of samples

weights : {int: {int: float}}, NoneOptional[Dict[int, Dict[int, float]]] (default: None)

Weights to use for comparing states.

missing_state_indicator : intint (default: -1)

State indicating missing data

Return type

arrayarray

Returns

A dissimilarity mapping as a flattened array.

cassiopeia.data.CassiopeiaTree cassiopeia.data.get_lca_characters