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Seurat (version 5.0.3)

FindBridgeAnchor: Find bridge anchors between two unimodal datasets

Description

First, bridge object is used to reconstruct two single-modality profiles and then project those cells into bridage graph laplacian space. Next, find a set of anchors between two single-modality objects. These anchors can later be used to integrate embeddings or transfer data from the reference to query object using the MapQuery object.

Usage

FindBridgeAnchor(
  object.list,
  bridge.object,
  object.reduction,
  bridge.reduction,
  anchor.type = c("Transfer", "Integration"),
  reference = NULL,
  laplacian.reduction = "lap",
  laplacian.dims = 1:50,
  reduction = c("direct", "cca"),
  bridge.assay.name = "Bridge",
  reference.bridge.stored = FALSE,
  k.anchor = 20,
  k.score = 50,
  verbose = TRUE,
  ...
)

Value

Returns an AnchorSet object that can be used as input to IntegrateEmbeddings.or MapQuery

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

anchor.type

The type of anchors. Can be one of:

  • Integration: Generate IntegrationAnchors for integration

  • Transfer: Generate TransferAnchors for transfering data

reference

A vector specifying the object/s to be used as a reference during integration or transfer data.

laplacian.reduction

Name of bridge graph laplacian dimensional reduction

laplacian.dims

Dimensions used for bridge graph laplacian dimensional reduction

reduction

Dimensional reduction to perform when finding anchors. Can be one of:

  • cca: Canonical correlation analysis

  • direct: Use assay data as a dimensional reduction

bridge.assay.name

Assay name used for bridge object reconstruction value (default is 'Bridge')

reference.bridge.stored

If refernece has stored the bridge dictionary representation

k.anchor

How many neighbors (k) to use when picking anchors

k.score

How many neighbors (k) to use when scoring anchors

verbose

Print messages and progress

...

Additional parameters passed to FindIntegrationAnchors or FindTransferAnchors

Details

  • Bridge cells reconstruction

  • Find anchors between objects. It can be either IntegrationAnchors or TransferAnchor.