autogenes.Interface.init

Interface.init(data, celltype_key = 'celltype', genes_key = None, use_highly_variable = False)

Preprocesses input data

If an AnnData object is passed, it is assumed that it contains single-cell data. The means are calculated using ‘celltype_key’. In addition, a pre-selection of genes can be specified with ‘genes_key’ or ‘use_highly_variable’. Then, only these genes will be considered in the optimization.

If a DataFrame or numpy array is passed, it is assumed that they already contain the means.

Parameters

• data (anndata.AnnData, np.ndarray, pd.DataFrame) – Input data

• celltype_key (str, optional (default: celltype)) – Name of the obs column that specifies the cell type of a cell For AnnData only

• genes_key (str, optional (default: None)) – Name of the var column with boolean values to pre-select genes

• use_highly_variable (bool, optional (default: False)) – Equivalent to genes_key=’highly_variable’

Returns

None