mmc.Hierarchy.publication_export()

Hierarchy.publication_export(adata=None, batches=None, data_key=None, filepath='')

Creates a formatted csv files of your hierarchy, including its high confidence definitions and thresholds. The resulting file will have two sheets, one with subset name, parent subset, positive features, and negative features. The other with thresholds for each marker for each of the batches.

Currently in beta. Assumes no “+” symbol present in feature names. Does not support categorical value cutoff layers (i.e. not True/False).

Parameters:

• adata (Optional[AnnData] (default: None)) – Adata to use to lookup gene names, with genes in the .X,

• batches (Optional[List[str]] (default: None)) – A list of batches to find thresholds for. If None, just creates thresholds for a single batch

• data_key (Union[str, list, None] (default: None)) – Used to point to a key in .obsm or .var[utils.MODALITY_COLUMN] to check for marker names

• filepath (str (default: '')) – path where the csv files are saved