dynamo.vf.rank_sensitivity_genes
- dynamo.vf.rank_sensitivity_genes(adata, groups=None, skey='sensitivity_pca', abs=False, mode='full reg', exclude_diagonal=False, **kwargs)[source]
Rank genes or gene-gene interactions based on their sensitivity elements for each cell group.
Run .vf.sensitivity and set store_in_adata=True before using this function.
- Parameters
adata (
AnnData) – AnnData object that contains the reconstructed vector field in the .uns attribute.groups (str or None (default: None)) – Cell groups used to group the sensitivity.
skey (str (default: 'sensitivity_pca')) – The key of the stored sensitivity in .uns.
abs (bool (default: False)) – Whether or not to take the absolute value of the Jacobian.
mode ({'full reg', 'full eff', 'reg', 'eff', 'int'} (default: 'full_reg')) – The mode of ranking: (1) ‘full reg’: top regulators are ranked for each effector for each cell group; (2) ‘full eff’: top effectors are ranked for each regulator for each cell group; (3) ‘reg’: top regulators in each cell group; (4) ‘eff’: top effectors in each cell group; (5) ‘int’: top effector-regulator pairs in each cell group.
exclude_diagonal (bool (default: False)) – Whether to consider the self-regulation interactions (diagnoal of the jacobian matrix)
kwargs – Keyword arguments passed to ranking functions.
- Returns
adata – AnnData object which has the rank dictionary in .uns.
- Return type