lynx.dataset.HeteroDataset

class lynx.dataset.HeteroDataset(*args, **kwargs)

Bases: XeniumDataset

Load paired multi-modal ST data w/ hybrid resolutions into a hetero-graph

Parameters:

• adatas_ref (scanpy.AnnData | List[scanpy.AnnData])

• adatas_query (scanpy.AnnData | List[scanpy.AnnData])

• k (int)

• r (float)

• r_bigraph (float)

• n_subgraphs (int)

• is_query_grid (bool)

• is_ref_grid (bool)

__init__(adatas_ref, adatas_query, k=8, r=50.0, r_bigraph=30.0, n_subgraphs=8, is_query_grid=True, is_ref_grid=False, **kwargs)

Parameters:

• adatas_ref (scanpy.AnnData | List[scanpy.AnnData])

• adatas_query (scanpy.AnnData | List[scanpy.AnnData])

• k (int)

• r (float)

• r_bigraph (float)

• n_subgraphs (int)

• is_query_grid (bool)

• is_ref_grid (bool)

Methods

__init__(adatas_ref, adatas_query[, k, r, ...])
construct_graph(neighbor_nodes, distances[, ...])	Compute undirected graph edges & attributes
construct_hetero_graph(ref_neighbors, distances)	Compute ref -> query & query -> ref edges & attributes to construct hetero-graph, ref_neighbors - (dim: [L', k])
get(idx)
get_neighbors(ref_coords, query_coords[, ...])	Retrieve k-nearest-neighbor (or radius-bounded neighbors) of query_coords to ref_coords using a KDTree
len()
load_graphs()

construct_hetero_graph(ref_neighbors, distances)

Compute ref -> query & query -> ref edges & attributes to construct hetero-graph, ref_neighbors - (dim: [L’, k])