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