get_neighborhood_signal: Method dispatch function for neighborhood selection

In patrickCNMartin/Vesalius: Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data

Method dispatch function for neighborhood selection

Description

Method dispatch function for neighborhood selection

Usage

get_neighborhood_signal(coord, signal, method, k = 20, depth = 3, radius = 20)

Arguments

coord	data.frame - coordinates of assay (barcodes, x, y)
signal	matrix - matrix or sparse matrix containing assay signal for all spatial indices contained in coord
method	character - which method should be use to collect neighborhood - switch matches
k	int - how many nearest neighbors from KNN algorithm
depth	int - graph path depth to define neighborhood 0 = self, 1 = direct neigbors, 2 = neighbors of neighbors, etc
radius	- numeric - radius around center cell

Value

matrix of average signals for each spatial index and its neighborhood.

patrickCNMartin/Vesalius documentation built on April 17, 2025, 11:31 p.m.