cell_clone_coembed

Construct Cell-Cell Distance Matrix via Clone-Aware Coembedding

Usage

cell_clone_coembed(cell_embedding, clone_embedding, cell_k = 30, clone_k = 15)

Arguments

cell_embedding

A numeric matrix of cell embeddings (rows = cells).

clone_embedding

A numeric matrix of clone embeddings (rows = clones).

cell_k

Integer. Number of neighbors to compute for cell-level kNN (default: 30).

clone_k

Integer. Number of neighbors to compute for clone-level kNN (default: 15).

Value

A symmetric sparse distance matrix (class `dgCMatrix`) encoding clone-informed cell-cell distances.

Details

Integrates cell and clone embeddings by using clone-level proximity to reweight cell-cell distances. Generates a sparse distance matrix suitable for downstream embedding or trajectory inference.