cassiopeia.tl.fitch_hartigan#

cassiopeia.tl.fitch_hartigan(cassiopeia_tree, meta_item, root=None, state_key='S1', label_key='label', copy=False)[source]#

Run the Fitch-Hartigan algorithm.

Performs the full Fitch-Hartigan small parsimony algorithm which, given a set of states for the leaves, infers the most-parsimonious set of states and returns a random solution that satisfies the maximum-parsimony criterion. The solution will be stored in the label key specified by the user (by default ‘label’). This function will modify the tree in place if copy=False.

Parameters:

cassiopeia_tree CassiopeiaTree: CassiopeiaTree that has been processed with the Fitch-Hartigan bottom-up algorithm.
meta_item str: A column in the CassiopeiaTree cell meta corresponding to a categorical variable.
root Optional[str] (default: None): Root from which to begin this refinement. Only the subtree below this node will be considered.
state_key str (default: 'S1'): Attribute key that stores the Fitch-Hartigan ancestral states.
label_key str (default: 'label'): Key to add that stores the maximum-parsimony assignment inferred from the Fitch-Hartigan top-down refinement.
copy bool (default: False): Modify the tree in place or not.

Return type:

Optional[CassiopeiaTree]

Returns:

A new CassiopeiaTree if the copy is set to True, else None.