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, 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 : AnnData

Annotated data matrix.

layout : str, optional (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 or None, optional (default: None)

Root for tree layouts.

random_state : int or None, optional (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 : sparse matrix or None, optional (default: None)

Sparse adjacency matrix of the graph, defaults to adata.uns['neighbors']['connectivities'].

key_ext : str, optional (default: None)

By default, append layout.

proceed : bool, optional (default: None)

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

init_pos : {‘paga’, any valid 2d-.obsm key, False}, optional (default: False)

Use precomputed coordinates for initialization.

copy : bool (default: False)

Return a copy instead of writing to adata.

**kwds : further parameters

Parameters of chosen igraph layout. See, e.g., fruchterman_reingold. One of the most important ones is maxiter.
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’