This function will construct a new assay where each feature is a cell label. The values represent the sum of a particular cell label neighboring a given cell.
Usage
BuildNicheAssay(
object,
fov,
group.by,
assay = "niche",
cluster.name = "niches",
neighbors.k = 20,
niches.k = 4,
...
)Arguments
- object
A Seurat object
- fov
FOV object to gather cell positions from
- group.by
Cell classifications to count in spatial neighborhood
- assay
Name for spatial neighborhoods assay
- cluster.name
Name of output clusters
- neighbors.k
Number of neighbors to consider for each cell
- niches.k
Number of niche clusters to construct
- ...
Extra parameters passed to
kmeans