FACSPy.ml.unsupervisedGating.identify_populations

unsupervisedGating.identify_populations(cluster_kwargs=None)

Parameters:

cluster_kwargs (Optional[dict]) – keyword arguments passed to the respective cluster function.

Return type:

modifies AnnData object where the identified populations are stored in adata.obsm[“gating”].

Examples

>>> import FACSPy as fp
>>> dataset = fp.dt.create_dataset(...)
>>> gating_strategy = {"T_cells": ["CD45+", ["CD3+"]]}
>>> clf = fp.ml.unsupervisedGating(
...     dataset,
...     gating_strategy = gating_strategy,
...     layer = "transformed",
...     clustering_algorithm = "parc"
... )
>>> clf.identify_populations()