pytometry.preprocessing.compensate

pytometry.preprocessing.compensate(adata, comp_matrix=None, matrix_type='spillover', inplace=True)

Computes compensation for data channels.

Parameters

• adata (AnnData) – AnnData object

• key (str, optional) – key where result vector is added to the adata.var. Defaults to ‘signal_type’.

• comp_matrix (pd.DataFrame, optional) – a custom compensation matrix. Please note that by default we use the spillover matrix directly for numeric stability.

• matrix_type (str, optional) – whether to use a spillover matrix (default) or a compensation matrix. Only considered for custom compensation matrices. Usually, custom compensation matrices are the inverse of the spillover matrix. If you want to use a compensation matrix, not the spillover matrix, set matrix_type to compensation.

• inplace (bool, optional) – Return a copy instead of writing to adata. Defaults to True.

Return type

Optional[AnnData]

Returns

Depending on inplace, returns or updates adata

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