niche_composition: Method dispatch function for neighborhood selection - added...

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

Method dispatch function for neighborhood selection - added flavor specific to composition

Description

Method dispatch function for neighborhood selection - added flavor specific to composition

Usage

niche_composition(
  coord,
  vesalius_assay,
  method,
  cell_label = NULL,
  k = 20,
  depth = 3,
  radius = 20
)

Arguments

coord	data.frame - coordinates of assay (barcodes, x, y)
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
signal	matrix - matrix or sparse matrix containing assay signal for all spatial indices contained in coord

Value

list of all cells and cell types for each niche

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