rapids_singlecell.tl.draw_graph

rapids_singlecell.tl.draw_graph#

rapids_singlecell.tl.draw_graph(adata, *, init_pos=None, max_iter=500, random_state=0)[source]#

Force-directed graph drawing [FR91, JVHB14].

Uses cugraph’s implementation of Force Atlas 2. This is a reimplementation of scanpys function for GPU compute.

Parameters:

adata AnnData: annData object with ‘neighbors’ field.
init_pos 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.
max_iter int (default: 500): This controls the maximum number of levels/iterations of the Force Atlas algorithm. When specified the algorithm will terminate after no more than the specified number of iterations. No error occurs when the algorithm terminates in this manner. Good short-term quality can be achieved with 50-100 iterations. Above 1000 iterations is discouraged.
random_state int | None (default: 0): Random state to use when initializing layout and generating samples. Defaults to 0. If None is passed, a hash of process id, time, and hostname is used by cugraph.

Return type:

None

Returns:

updates adata with the following fields.