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weight_matrix with n_nearest_neighbors and n_neighbors #5

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wyq977 opened this issue Jan 5, 2023 · 1 comment

Contributor

wyq977 commented Jan 5, 2023

Hi, I am wondering why there are two parameters for nearest neighbours in weight matrix calculation.

SpatialDM/spatialdm/main.py

Line 34 in aa17624

    
           def weight_matrix(adata, l, cutoff=None, n_neighbors=None, n_nearest_neighbors=6, single_cell=False):

It seems to me that there is no need for both or am I missing sth?

Best

Collaborator

leeyoyohku commented Jan 11, 2023

n_neighbors is for secreted (long-distance) signaling, while n_nearest_neighbors is for adjacent signaling (ECM or cell-cell contact).

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