grassp.tl.leiden_mito_sweep

leiden_mito_sweep(data, starting_resolution=0.5, resolution_increments=0.5, min_mito_fraction=0.9, increment_threshold=0.005, protein_ground_truth_column='protein_ground_truth', **leiden_kwargs)

Automated sweep to pick a Leiden resolution that keeps mitochondria intact.

Starting from starting_resolution the function iteratively increases or decreases the resolution (binary-search style) until mitochondrial proteins—identified via protein_ground_truth_column—remain grouped in a single Leiden cluster with at least min_mito_fraction of all mitochondrial proteins.

The final resolution and the observed fraction are stored in data.uns['leiden']['params']['resolution'] and data.uns['leiden']['mito_majority_fraction'].

Parameters:

data AnnData

anndata.AnnData object after scanpy.pp.neighbors() with proteins as observations.

starting_resolution float (default: 0.5)

Initial Leiden resolution from which to begin the sweep.

resolution_increments float (default: 0.5)

Step size added (or subtracted) each iteration; halved whenever the sweep crosses the min_mito_fraction threshold.

min_mito_fraction float (default: 0.9)

Required proportion of mitochondrial proteins that must share a cluster (default 0.9).

increment_threshold float (default: 0.005)

When the increment falls below this value the search terminates.

protein_ground_truth_column str (default: 'protein_ground_truth')

Observation column holding the curated ground-truth localisation with the category "mitochondria".

**leiden_kwargs

Extra parameters forwarded to scanpy.tl.leiden() (e.g. random_state).

Return type:

None

Returns:

Updates data.obs['leiden'] and data.uns['leiden'] in place.