scanpy.tl.draw_graph

scanpy.tl.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)

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 : AnnDataAnnData

Annotated data matrix.

layout : {‘fr’, ‘drl’, ‘kk’, ‘grid_fr’, ‘lgl’, ‘rt’, ‘rt_circular’, ‘fa’}Literal[‘fr’, ‘drl’, ‘kk’, ‘grid_fr’, ‘lgl’, ‘rt’, ‘rt_circular’, ‘fa’] (default: '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).

root : int | NoneOptional[int] (default: None)

Root for tree layouts.

random_state : None | int | RandomStateUnion[None, int, RandomState] (default: 0)

For layouts with random initialization like ‘fr’, change this to use different intial states for the optimization. If None, no seed is set.

adjacency : spmatrix | NoneOptional[spmatrix] (default: None)

Sparse adjacency matrix of the graph, defaults to neighbors connectivities.

key_added_ext : str | NoneOptional[str] (default: None)

By default, append layout.

proceed

Continue computation, starting off with ‘X_draw_graph_`layout`’.

init_pos : str | bool | NoneUnion[str, bool, None] (default: None)

'paga'/True, None/False, or any valid 2d-.obsm key. Use precomputed coordinates for initialization. If False/None (the default), initialize randomly.

neighbors_key : str | NoneOptional[str] (default: None)

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 : str | NoneOptional[str] (default: None)

Use .obsp[obsp] as adjacency. You can’t specify both obsp and neighbors_key at the same time.

copy : boolbool (default: False)

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.

Returns

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

X_draw_graph_layoutadata.obsm

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