netmap.masking.internal.create_pairwise_binary_mask

netmap.masking.internal.create_pairwise_binary_mask(binary_matrix, gene_list, source_list, target_list)[source]

Creates a dense 2D array of pairwise masks using preallocation.

Edge genes are passed as separate source_list/target_list arrays rather than parsed from “GeneA_GeneB” strings, since gene names may themselves contain underscores and would make that split ambiguous.

Parameters:

  • binary_matrix (np.ndarray) – Rows=cells, Cols=genes.

  • gene_list (list) – The names of the genes in binary_matrix columns.

  • source_list (Sequence[str]) – Source gene of each requested edge, in the order the output columns should follow.

  • target_list (Sequence[str]) – Target gene of each requested edge, aligned with source_list.

Returns:

A 2D array of shape (num_cells, len(source_list)).

Return type:

np.ndarray