dynamo.vf.rank_jacobian_genes
- dynamo.vf.rank_jacobian_genes(adata, groups=None, jkey='jacobian_pca', abs=False, mode='full reg', exclude_diagonal=False, normalize=False, return_df=False, **kwargs)[source]
Rank genes or gene-gene interactions based on their Jacobian elements for each cell group.
Run .vf.jacobian 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 Jacobians.
jkey (str (default: 'jacobian_pca')) – The key of the stored Jacobians in .uns.
abs (bool (default: False)) – Whether take the absolute value of the Jacobian.
mode ({'full reg', 'full eff', 'reg', 'eff', 'int', 'switch'} (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. (6) ‘switch’: top effector-regulator pairs that show mutual inhibition pattern in each cell group.
exclude_diagonal (bool (default: False)) – Whether to consider the self-regulation interactions (diagnoal of the jacobian matrix)
normalize (bool (default: False)) – Whether normalize the Jacobian across all cells before performing the ranking.
return_df (bool (default: False)) – Whether to return the data or to save results in adata object via the key mode of adata.uns.
kwargs – Keyword arguments passed to ranking functions.
- Returns
different modes return different types of return values 1. full reg and full eff:
A pandas dataframe containing ranking info based on Jacobian elements
- reg eff int:
A dictionary object whose keys correspond to groups, and whose values are specific rank’s pd dataframe
- Return type
rank_info