arcfish.pp.pseudo_count

arcfish.pp.pseudo_count(adata: AnnData, threshold: float) → ndarray

Thresholding pairwise distances to create a count matrix.

Parameters:

• adata (AnnData) – Object created by FOF_CT_Loader.create_adata().

• threshold (float) – Entries with pairwise distance smaller than this threshold are considered as a count.

Returns:

p by p pseudo count matrix.

Return type:

np.ndarray