BuildNicheAssay: Construct an assay for spatial niche analysis

In satijalab/seurat: Tools for Single Cell Genomics

Construct an assay for spatial niche analysis

Description

This function will construct a new assay where each feature is a cell label The values represents 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 clusters to return based on the niche assay

Value

Seurat object containing a new assay

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.