harreman.preprocessing.setup_deconv_adata

harreman.preprocessing.setup_deconv_adata(adata, compute_neighbors_on_key=None, sample_key=None, cell_type_list=None, cell_type_key=None, spot_diameter=None, verbose=False)

Set up deconvolution AnnData.

Parameters:

• adata (AnnData) – AnnData object.

• compute_neighbors_on_key (Optional[str] (default: None)) – Key in adata.obsm to use for computing neighbors. If None, use neighbors stored in adata. If no neighbors have been previously computed an error will be raised.

• sample_key (Optional[str] (default: None)) – Sample information in case the data contains different samples or samples from different conditions. Input is key in adata.obs.

• cell_type_list (Optional[list] (default: None)) – Cell type or cluster information for the cell-cell communication analysis. Input is a list of keys in adata.layers.

• cell_type_key (Optional[str] (default: None)) – Cell type or cluster information for the cell-cell communication analysis. Input is key in adata.obs.

• spot_diameter (Optional[int] (default: None)) – Spot diameter of the spatial technology the dataset belongs to.

• verbose (bool, optional (default: False)) – Whether to print progress and status messages.