cytonormpy.emd_from_anndata

cytonormpy.emd_from_anndata#

cytonormpy.emd_from_anndata(adata, file_list, channels, layer, sample_identifier_column='file_name', cell_labels=None, origin=None, transformer=None)#

Function to evaluate the EMD on an AnnData file.

Parameters:

  • adata (AnnData) – The AnnData object

  • file_list (Union[list[str], str]) – A list of files. Used in conjunction with sample_identifier_column.

  • channels (Optional[list[str]]) – A list of detectors to analyze.

  • layer (str) – The layer where the data are stored.

  • sample_identifier_column (str) – Specifies the column in adata.obs in which the samples are identified.

  • labels (cell) – Specifies the column in adata.obs containing cell labels. The cell labels will be added to the dataframe. If None, MADs will be calculated per file and channel.

  • groupby – Specify on what the MADs should be grouped. Can be “file_name”, “label” or [“file_name”, “label”].

  • origin (Optional[str]) – Annotates the files with their origin, e.g. ‘original’ or ‘normalized’.

  • transformer (Optional[Transformer]) – An instance of the cytonormpy transformers.

Return type:

A pandas.DataFrame containing the MAD values per file or per file and cell_label.

Contents