SC2Spa.tl.NRD_impute

SC2Spa.tl.NRD_impute(neighbors, dis, adata_ref, adata_query, ct_name=None, weight_constant=1, exclude_CTs=None)

Reconstruct the gene expression profile of ST beads based on the NRD_weight output

Predicted cell type proportion will be saved in adata_ref.obs.

Parameters

neighbors

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

dis

corresponding distance matrix of the neighbor matrix

adata_ref

Reference anndata object. Gene expression matrix should be the shape of (cell, gene). Predicted coordinates should be stored in adata_ref.obs[[‘x_transfer’, ‘y_transfer’]]

adata_query

Query anndata object. Gene expression matrix should be the shape of (cell, gene). Cell type annotation should be stored in adata_query.obs[ct_name] Predicted locations should be stored in adata_query.obs[[‘x_transfer’, ‘y_transfer’]]

dis_min

Distance cutoff that determines if a ST bead and a single cell is paired

exclude_CTs

A list that contains cell types to be excluded

Returns

adata_impute

An Anndata object that stores the reconstructed gene expression profile of ST beads