scfocus.utils.run_focus

scfocus.utils.run_focus(_embedding, n=6, pct_samples=0.01, meta_focusing=3)

Run scFocus analysis on embedding data.

Parameters:

• _embedding (numpy.ndarray) – 2D embedding coordinates (e.g., from UMAP or t-SNE).

• n (int, optional) – Number of parallel agents/branches to identify (default: 6).

• pct_samples (float, optional) – Percentage of samples to use in each training step (default: 0.01).

• meta_focusing (int, optional) – Number of meta-focusing iterations (default: 3).

Returns:

focus_probs – Matrix of focus probabilities with shape (n_cells, n_branches).

Return type:

numpy.ndarray

Notes

This function creates a scFocus object, performs meta-focusing iterations, merges focus patterns, and returns the final focus probability matrix. Results are cached to avoid redundant computations.