FACSPy.dt.calculate_cofactors

FACSPy.dt.calculate_cofactors#

FACSPy.dt.calculate_cofactors(adata, add_to_adata=True, return_dataframe=False, copy=False)#

Calculates the cofactors based on the channel histograms.

Parameters:

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

  • add_to_adata (bool) – Whether to add the calculated cofactors to the adata object. Defaults to True.

  • return_dataframe (bool) – Whether to return the calculated cofactors as a pd.DataFrame. Defaults to False

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

Return type:

Optional[AnnData, tuple[CofactorTable, DataFrame]]]

Returns:

  • If copy is True – The AnnData object. If add_to_adata is True, the .uns[‘cofactors’] and .uns[‘raw_cofactors’] slots are filled with the corresponding tables.

  • If return_dataframe – a tuple of the cofactor table and the raw cofactors per sample

Examples

>>> import FACSPy as fp
>>> dataset = fp.create_dataset(...)
>>> dataset
AnnData object with n_obs × n_vars = 615936 × 22
obs: 'sample_ID', 'file_name', 'condition'
var: 'pns', 'png', 'pne', 'pnr', 'type', 'pnn'
uns: 'metadata', 'panel', 'workspace', 'gating_cols', 'dataset_status_hash'
obsm: 'gating'
layers: 'compensated'
>>> fp.calculate_cofactors(dataset)
>>> dataset
AnnData object with n_obs × n_vars = 615936 × 22
obs: 'sample_ID', 'file_name', 'condition'
var: 'pns', 'png', 'pne', 'pnr', 'type', 'pnn'
uns: 'metadata', 'panel', 'workspace', 'gating_cols', 'dataset_status_hash',
'raw_cofactors', 'cofactors'
obsm: 'gating'
layers: 'compensated'
>>> fp.transform(
...     dataset,
...     transform = "asinh",
...     cofactor_table = dataset.uns["cofactors"],
...     key_added = "transformed"
... )
>>> dataset
AnnData object with n_obs × n_vars = 615936 × 22
obs: 'sample_ID', 'file_name', 'condition'
var: 'pns', 'png', 'pne', 'pnr', 'type', 'pnn'
uns: 'metadata', 'panel', 'workspace', 'gating_cols', 'dataset_status_hash',
'raw_cofactors', 'cofactors'
obsm: 'gating'
layers: 'compensated', 'transformed'
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