ehrapy.tools.draw_graph

ehrapy.tools.draw_graph(adata, layout='fa', init_pos=None, root=None, random_state=0, n_jobs=None, adjacency=None, key_added_ext=None, neighbors_key=None, obsp=None, copy=False, **kwds)[source]

Force-directed graph drawing [Islam11] [Jacomy14] [Chippada18].

An alternative to tSNE that often preserves the topology of the data better. This requires to run neighbors(), first. The default layout (‘fa’, ForceAtlas2) [Jacomy14] uses the package fa2 [Chippada18], which can be installed via pip install fa2. Force-directed graph drawing describes a class of long-established algorithms for visualizing graphs. It has been suggested for visualizing single-cell data by [Islam11]. Many other layouts as implemented in igraph [Csardi06] are available. Similar approaches have been used by [Zunder15] or [Weinreb17].

Parameters:

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

  • layout (Literal['fr', 'drl', 'kk', 'grid_fr', 'lgl', 'rt', 'rt_circular', 'fa']) – ‘fa’ (ForceAtlas2) or any valid igraph layout. Of particular interest are ‘fr’ (Fruchterman Reingold), ‘grid_fr’ (Grid Fruchterman Reingold, faster than ‘fr’), ‘kk’ (Kamadi Kawai’, slower than ‘fr’), ‘lgl’ (Large Graph, very fast), ‘drl’ (Distributed Recursive Layout, pretty fast) and ‘rt’ (Reingold Tilford tree layout).

  • init_pos (Union[str, bool, None]) – ‘paga’/True, None/False, or any valid 2d-.obsm key. Use precomputed coordinates for initialization. If False/None (the default), initialize randomly.

  • root (Optional[int]) – Root for tree layouts.

  • random_state (Union[int, RandomState, None]) – For layouts with random initialization like ‘fr’, change this to use different intial states for the optimization. If None, no seed is set.

  • n_jobs (Optional[int]) – Number of jobs for parallel computation. None means using scanpy._settings.ScanpyConfig.n_jobs.

  • adjacency (Optional[spmatrix]) – Sparse adjacency matrix of the graph, defaults to neighbors connectivities.

  • key_added_ext (Optional[str]) – By default, append layout.

  • neighbors_key (Optional[str]) – If not specified, draw_graph looks .obsp[‘connectivities’] for connectivities (default storage place for pp.neighbors). If specified, draw_graph looks .obsp[.uns[neighbors_key][‘connectivities_key’]] for connectivities.

  • obsp (Optional[str]) – Use .obsp[obsp] as adjacency. You can’t specify both obsp and neighbors_key at the same time.

  • copy (bool) – Whether to return a copy instead of writing to adata.

  • **kwds – Parameters of chosen igraph layout. See e.g. fruchterman-reingold [Fruchterman91]. One of the most important ones is maxiter.

Return type:

Optional[AnnData]

Returns:

Depending on copy, returns or updates adata with the following field.

X_draw_graph_layout : adata.obsm Coordinates of graph layout. E.g. for layout=’fa’ (the default), the field is called ‘X_draw_graph_fa’