FACSPy.subset_gate

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FACSPy.subset_gate#

FACSPy.subset_gate(adata, gate, as_view=False, copy=False)#

Subsets the dataset to a specific population.

Parameters:

  • adata (AnnData) – The anndata object of shape n_obs x n_vars where rows correspond to cells and columns to the channels.

  • gate (str) – The gate to be subset to. Can be passed as a population name (e.g. ‘CD45+’), a partial gate path (e.g. ‘live/CD45+’) or a complete gate path (e.g. ‘root/cells/live/CD45+’)

  • as_view (bool) – If True, returns an AnnDataView object.

  • copy (bool) – Whether to copy the dataset.

Return type:

AnnData or None, depending on copy.

Examples

>>> import FACSPy as fp
>>> dataset = fp.create_dataset(...)
>>> fp.subset_gate(dataset, "CD45+")

>>> import FACSPy as fp
>>> dataset = fp.create_dataset(...)
>>> fp.subset_gate(dataset, 'live/CD45+')

>>> import FACSPy as fp
>>> dataset = fp.create_dataset(...)
>>> fp.subset_gate(dataset, 'root/cells/live/CD45+')
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