Seurat (version 5.0.3)

BridgeCellsRepresentation: 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
)

Value

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

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