Method dispatch function for neighborhood selection - added flavor specific to composition
Source:R/map_assays.R
niche_composition.RdMethod 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