Perform dataset integration using a pre-computed Anchorset of specified low dimensional representations.
IntegrateEmbeddings(anchorset, ...) # S3 method for IntegrationAnchorSet IntegrateEmbeddings( anchorset, new.reduction.name = "integrated_dr", reductions = NULL, dims.to.integrate = NULL, k.weight = 100, weight.reduction = NULL, sd.weight = 1, sample.tree = NULL, preserve.order = FALSE, verbose = TRUE, ... ) # S3 method for TransferAnchorSet IntegrateEmbeddings( anchorset, reference, query, query.assay = NULL, new.reduction.name = "integrated_dr", reductions = "pcaproject", dims.to.integrate = NULL, k.weight = 100, weight.reduction = NULL, reuse.weights.matrix = TRUE, sd.weight = 1, preserve.order = FALSE, verbose = TRUE, ... )
An AnchorSet object
Reserved for internal use
Name for new integrated dimensional reduction.
Name of reductions to be integrated. For a
TransferAnchorSet, this should be the name of a reduction present in the
anchorset object (for example, "pcaproject"). For an IntegrationAnchorSet,
this should be a
DimReduc object containing all cells present
in the anchorset object.
Number of dimensions to return integrated values for
Number of neighbors to consider when weighting anchors
Dimension reduction to use when calculating anchor weights. This can be one of:
A string, specifying the name of a dimension reduction present in all objects to be integrated
A vector of strings, specifying the name of a dimension reduction to use for each object to be integrated
A vector of
DimReduc objects, specifying the object to
use for each object in the integration
NULL, in which case the full corrected space is used for computing anchor weights.
Controls the bandwidth of the Gaussian kernel for weighting
Specify the order of integration. Order of integration
should be encoded in a matrix, where each row represents one of the pairwise
integration steps. Negative numbers specify a dataset, positive numbers
specify the integration results from a given row (the format of the merge
matrix included in the
hclust function output). For example:
matrix(c(-2, 1, -3, -1), ncol = 2) gives:
Which would cause dataset 2 and 3 to be integrated first, then the resulting object integrated with dataset 1.
If NULL, the sample tree will be computed automatically.
Do not reorder objects based on size for each pairwise integration.
Print progress bars and output
Reference object used in anchorset construction
Query object used in anchorset construction
Name of the Assay to use from query
Can be used in conjunction with the store.weights parameter in TransferData to reuse a precomputed weights matrix.
When called on a TransferAnchorSet (from FindTransferAnchors), this will return the query object with the integrated embeddings stored in a new reduction. When called on an IntegrationAnchorSet (from IntegrateData), this will return a merged object with the integrated reduction stored.
The main steps of this procedure are identical to
with one key distinction. When computing the weights matrix, the distance
calculations are performed in the full space of integrated embeddings when
integrating more than two datasets, as opposed to a reduced PCA space which
is the default behavior in