netmap.downstream.clustering.downstream_recipe¶

netmap.downstream.clustering.downstream_recipe(grn_adata, config={'knn_neighbors': 50, 'leiden_resolution': 0.1, 'min_cells': 1, 'n_components': 100, 'n_neighbors': 30}) → AnnData¶

Minimal downstream processing for GRN object. Runs sc.pca (without scaling), sc.neighbours, sc.leiden, sc. umap

Parameters:

grn_adata (AnnData) – A GRN anndata object to process
config (dict) – Parameters for the processing

Returns:

grn_adata – Processed Anndata object

Return type:

AnnData