SC2Spa.tl.NRD_CT_preprocess

SC2Spa.tl.NRD_CT_preprocess(adata_ref, adata_query, n_neighbors=1000, dis_cutoff=15)

Apply KNN algorithm to obtain the single cell neighbors of ST beads

Parameters

adata_ref

Reference anndata object. Gene expression matrix should be the shape of (cell, gene). The predicted coordinates of beads should be stored in adata_ref.obsm[‘spatial_mapping’]

adata_query

Query anndata object. Gene expression matrix should be the shape of (cell, gene). The predicted coordinates of single cells should be stored in adata_query.obsm[‘spatial_mapping’].

n_neighbors

Number of the nearest neighbors of a bead or cell. This parameter is for the KNN algorithm

dis_cutoff

Maximum distance between a single cell and a ST bead. Only the cells within the cutoff

will be retained for further analysis.

Returns

neighbors_st

A matrix of single cell neighbors of ST beads with the shape of (n_beads, n_neighbors)

dis_st

The distance matrix of the neighbor matrix