FindBridgeAnchor.Rd
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/integration.R
\name{FindBridgeAnchor}
\alias{FindBridgeAnchor}
\title{Find bridge anchors between two unimodal datasets}
\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,
...
)
}
\arguments{
\item{object.list}{A list of Seurat objects}
\item{bridge.object}{A multi-omic bridge Seurat which is used as the basis to
represent unimodal datasets}
\item{object.reduction}{A list of dimensional reductions from object.list used
to be reconstructed by bridge.object}
\item{bridge.reduction}{A list of dimensional reductions from bridge.object used
to reconstruct object.reduction}
\item{anchor.type}{The type of anchors. Can
be one of:
\itemize{
\item{Integration: Generate IntegrationAnchors for integration}
\item{Transfer: Generate TransferAnchors for transfering data}
}}
\item{reference}{A vector specifying the object/s to be used as a reference
during integration or transfer data.}
\item{laplacian.reduction}{Name of bridge graph laplacian dimensional reduction}
\item{laplacian.dims}{Dimensions used for bridge graph laplacian dimensional reduction}
\item{reduction}{Dimensional reduction to perform when finding anchors. Can
be one of:
\itemize{
\item{cca: Canonical correlation analysis}
\item{direct: Use assay data as a dimensional reduction}
}}
\item{bridge.assay.name}{Assay name used for bridge object reconstruction value (default is 'Bridge')}
\item{reference.bridge.stored}{If refernece has stored the bridge dictionary representation}
\item{k.anchor}{How many neighbors (k) to use when picking anchors}
\item{k.score}{How many neighbors (k) to use when scoring anchors}
\item{verbose}{Print messages and progress}
\item{...}{Additional parameters passed to \code{FindIntegrationAnchors} or
\code{FindTransferAnchors}}
}
\value{
Returns an \code{\link{AnchorSet}} object that can be used as input to
\code{\link{IntegrateEmbeddings}}.or \code{\link{MapQuery}}
}
\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 \code{\link{MapQuery}} object.
}
\details{
\itemize{
\item{ Bridge cells reconstruction
}
\item{ Find anchors between objects. It can be either IntegrationAnchors or TransferAnchor.
}
}
}
\keyword{internal}