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.
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,
...
)Returns an AnchorSet object that can be used as input to
IntegrateEmbeddings.or MapQuery
A list of Seurat objects
A multi-omic bridge Seurat which is used as the basis to represent unimodal datasets
A list of dimensional reductions from object.list used to be reconstructed by bridge.object
A list of dimensional reductions from bridge.object used to reconstruct object.reduction
The type of anchors. Can be one of:
Integration: Generate IntegrationAnchors for integration
Transfer: Generate TransferAnchors for transfering data
A vector specifying the object/s to be used as a reference during integration or transfer data.
Name of bridge graph laplacian dimensional reduction
Dimensions used for bridge graph laplacian dimensional reduction
Dimensional reduction to perform when finding anchors. Can be one of:
cca: Canonical correlation analysis
direct: Use assay data as a dimensional reduction
Assay name used for bridge object reconstruction value (default is 'Bridge')
If refernece has stored the bridge dictionary representation
How many neighbors (k) to use when picking anchors
How many neighbors (k) to use when scoring anchors
Print messages and progress
Additional parameters passed to FindIntegrationAnchors or
FindTransferAnchors
Bridge cells reconstruction
Find anchors between objects. It can be either IntegrationAnchors or TransferAnchor.