ehrapy.tools.paga

ehrapy.tools.paga(adata, groups=None, use_rna_velocity=False, model='v1.2', neighbors_key=None, copy=False)[source]

Mapping out the coarse-grained connectivity structures of complex manifolds [Wolf19].

By quantifying the connectivity of partitions (groups, clusters), partition-based graph abstraction (PAGA) generates a much simpler abstracted graph (PAGA graph) of partitions, in which edge weights represent confidence in the presence of connections. By tresholding this confidence in paga(), a much simpler representation of the manifold data is obtained, which is nonetheless faithful to the topology of the manifold. The confidence should be interpreted as the ratio of the actual versus the expected value of connections under the null model of randomly connecting partitions. We do not provide a p-value as this null model does not precisely capture what one would consider “connected” in real data, hence it strongly overestimates the expected value. See an extensive discussion of this in [Wolf19].

Note

Note that you can use the result of paga() in umap() and draw_graph() via init_pos=’paga’ to get embeddings that are typically more faithful to the global topology.

Parameters:

  • adata (AnnData) – AnnData object object containing all observations.

  • groups (Optional[str]) – Key for categorical in adata.obs. You can pass your predefined groups by choosing any categorical annotation of observations. Default: The first present key of ‘leiden’ or ‘louvain’.

  • model (Literal['v1.2', 'v1.0']) – The PAGA connectivity model.

  • neighbors_key (Optional[str]) – If not specified, paga looks .uns[‘neighbors’] for neighbors settings and .obsp[‘connectivities’], .obsp[‘distances’] for connectivities and distances respectively (default storage places for pp.neighbors). If specified, paga looks .uns[neighbors_key] for neighbors settings and .obsp[.uns[neighbors_key][‘connectivities_key’]], .obsp[.uns[neighbors_key][‘distances_key’]] for connectivities and distances respectively.

  • copy (bool) – Copy adata before computation and return a copy. Otherwise, perform computation in place and return None.

Return type:

Optional[AnnData]

Returns:

connectivities numpy.ndarray (adata.uns[‘connectivities’])

The full adjacency matrix of the abstracted graph, weights correspond to confidence in the connectivities of partitions.

connectivities_tree scipy.sparse.csr_matrix (adata.uns[‘connectivities_tree’])

The adjacency matrix of the tree-like subgraph that best explains the topology.

Notes: Together with a random walk-based distance measure (e.g. ehrapy.tl.dpt()) this generates a partial coordinatization of data useful for exploring and explaining its variation.