RunNeighborhoodToCell — RunNeighborhoodToCell • NICHES

RunNeighborhoodToCell

RunNeighborhoodToCell(
  sys.small,
  ground.truth,
  assay,
  meta.data.to.map,
  blend = "mean",
  edgelist,
  output_format
)

Arguments

sys.small	A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.
ground.truth	Ground truth signaling mechanisms present in sys.small.
assay	The assay to run the SCC transformation on. Defaults to "RNA."
meta.data.to.map	A character vector of metadata names present in the original object which will be carried to the NICHES objects
blend	Choice of linear operator to combine edges. Defaults to "mean", also accepts "sum"
edgelist	data.frame. Each row is an directional edge between two spatially connected cells
output_format	string. Choice of the output format. "seurat" will output a list of seurat objects, "raw" will output a list of lists with raw interaction matrix and compiled metadata