sainsc.utils.celltype_signatures

sainsc.utils.celltype_signatures(adata, *, celltype_col='leiden', agg_method='mean')

Calculate gene expression signatures per ‘celltype’.

Note, that this will make a dense copy of adata.X therefore potentially leading to large memory usage.

Parameters:

adata (AnnData)
celltype_col (str, optional) – Name of column in anndata.AnnData.obs containing cell-type information.
agg_method (str or Callable, optional) – Function to aggregate gene expression per cluster used by pandas.DataFrame.agg().

Returns:

pandas.DataFrame of gene expression aggregated per ‘celltype’.

Return type: