plastro.lineage_simulation.introduce_crispr_mutations

plastro.lineage_simulation.introduce_crispr_mutations(tree: TreeNode, number_of_cassettes: int = 100) → cassiopeia.data.CassiopeiaTree[source]

Simulate CRISPR mutations on a phylogenetic tree.

Uses Cassiopeia’s mutation simulation to add realistic CRISPR-based lineage tracing mutations to the tree structure.

Parameters:

tree (ete3.Tree) – Phylogenetic tree to add mutations to.
number_of_cassettes (int, optional) – Number of mutation sites, by default 100 so we can accurately resolve lineage relationships.

Returns:

Tree with simulated character matrix containing mutation data.

Return type:

cassiopeia.data.CassiopeiaTree

Examples

>>> from ete3 import Tree
>>> tree = Tree("((A,B),C);")
>>> cass_tree = introduce_crispr_mutations(tree)
>>> print(cass_tree.character_matrix.shape)

Notes

This function requires the Cassiopeia package for mutation simulation. The resulting character matrix will have cells as rows and mutation sites as columns, with values representing different mutation states.