Construct an assay for spatial niche analysis

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.

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

Value

Seurat object containing a new assay