FACSPy.convert_gate_to_obs

FACSPy.convert_gate_to_obs#

FACSPy.convert_gate_to_obs(adata, gate, key_added=None, copy=False)#

Converts the gate information stored in .obsm[“gating”] into an .obs column.

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 transfer. Must be in adata.uns[“gating_cols”]. Can be specified as a population, as a partial gate path or a full gate path. Also allows for gate aliasing. If a gate alias is provided, pass the key_added parameter in order to pass that alias forward. Otherwise, the full gate path is used for the .obs column.

  • key_added (Optional[str]) – The name of the corresponding .obs column. Positive events will be stored as specified in key_added, negative events will be stored as other.

  • 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.convert_gate_to_obs(dataset, "CD45+", key_added = "leukocytes")
>>> fp.tl.pca(dataset, gate = "live", layer = "compensated")
>>> fp.pl.pca(dataset, color = "leukocytes")
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