BridgeCellsRepresentation: Construct a dictionary representation for each unimodal...

In Seurat: Tools for Single Cell Genomics

Construct a dictionary representation for each unimodal dataset

Description

Construct a dictionary representation for each unimodal dataset

Usage

BridgeCellsRepresentation(
  object.list,
  bridge.object,
  object.reduction,
  bridge.reduction,
  laplacian.reduction = "lap",
  laplacian.dims = 1:50,
  bridge.assay.name = "Bridge",
  return.all.assays = FALSE,
  l2.norm = TRUE,
  verbose = TRUE
)

Arguments

object.list	A list of Seurat objects
bridge.object	A multi-omic bridge Seurat which is used as the basis to represent unimodal datasets
object.reduction	A list of dimensional reductions from object.list used to be reconstructed by bridge.object
bridge.reduction	A list of dimensional reductions from bridge.object used to reconstruct object.reduction
laplacian.reduction	Name of bridge graph laplacian dimensional reduction
laplacian.dims	Dimensions used for bridge graph laplacian dimensional reduction
bridge.assay.name	Assay name used for bridge object reconstruction value (default is 'Bridge')
return.all.assays	Whether to return all assays in the object.list. Only bridge assay is returned by default.
l2.norm	Whether to l2 normalize the dictionary representation
verbose	Print messages and progress

Value

Returns a object list in which each object has a bridge cell derived assay

Seurat documentation built on Nov. 18, 2023, 1:10 a.m.