FACSPy.tl.gate_frequencies_mem

FACSPy.tl.gate_frequencies_mem#

FACSPy.tl.gate_frequencies_mem(adata, copy=False)#

Calculates the gate frequencies as a percentage. Same as fp.tl.gate_frequencies but runs on the csr_matrix of .obsm[‘gating’]. This approach is slightly slower but much more memory efficient. Will eventually replace fp.tl.gate_frequencies().

Parameters:

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

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

Returns:

Returns adata if copy = True, otherwise adds fields to the anndata object:

.uns[‘gate_frequencies’]

The gate frequencies as a percentage of all parent gates.

Return type:

AnnData or None

Examples

>>> import FACSPy as fp
>>> dataset
AnnData object with n_obs × n_vars = 615936 × 22
obs: 'sample_ID', 'file_name', 'condition', 'sex'
var: 'pns', 'png', 'pne', 'pnr', 'type', 'pnn', 'cofactors'
uns: 'metadata', 'panel', 'workspace', 'gating_cols', 'dataset_status_hash'
obsm: 'gating'
layers: 'compensated', 'transformed'
>>> fp.tl.gate_frequencies_mem(dataset)
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