plastro.lineage_simulation.simulate_lineage_tracing

plastro.lineage_simulation.simulate_lineage_tracing(sim_ad: anndata.AnnData, terminal_ad: anndata.AnnData, latent_space_key: str = 'X_dc', number_of_cassettes: int = 100, save_to: str | None = None) → cassiopeia.data.CassiopeiaTree[source]

Simulate lineage tracing using Cassiopeia on single-cell data.

Builds a phylogenetic tree from latent space coordinates and simulates CRISPR-based lineage tracing to generate character matrices.

Parameters:

  • sim_ad (anndata.AnnData) – Complete simulated single-cell dataset.

  • terminal_ad (anndata.AnnData) – Subset containing only terminal/observed cells.

  • latent_space_key (str, optional) – Key in sim_ad.obsm containing latent space coordinates, by default ‘X_dc’.

  • number_of_cassettes (int, optional) – Number of mutation sites, by default 100 so we can accurately resolve lineage relationships.

  • save_to (str, optional) – Directory to save tree and results, by default None.

Returns:

Cassiopeia tree object with character matrix and phylogenetic structure.

Return type:

cassiopeia.data.CassiopeiaTree

Examples

>>> import plastro
>>> # Assume sim_ad contains full simulated data and terminal_ad contains observed cells
>>> cass_tree = plastro.simulate_lineage_tracing(sim_ad, terminal_ad, 'X_dc')
>>> character_matrix = cass_tree.character_matrix
>>> print(f"Character matrix shape: {character_matrix.shape}")

Notes

This function combines tree construction from phenotypic similarity with CRISPR mutation simulation to create realistic lineage tracing data that can be used for plasticity analysis.