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Seurat

IntegrateEmbeddings

Integrate low dimensional embeddings

Description

Perform dataset integration using a pre-computed Anchorset of specified low dimensional representations.

Usage

IntegrateEmbeddings(anchorset, ...)

## S3 method for class '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 class 'TransferAnchorSet'
IntegrateEmbeddings(
  anchorset,
  reference,
  query,
  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,
  ...
)

Arguments

anchorset

An AnchorSet object
...

Reserved for internal use
new.reduction.name

Name for new integrated dimensional reduction.
reductions

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.
dims.to.integrate

Number of dimensions to return integrated values for
k.weight

Number of neighbors to consider when weighting anchors
weight.reduction

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.

sd.weight

Controls the bandwidth of the Gaussian kernel for weighting
sample.tree

Specify the order of integration. If NULL, will compute automatically.
preserve.order

Do not reorder objects based on size for each pairwise integration.
verbose

Print progress bars and output
reference

Reference object used in anchorset construction
query

Query object used in anchorset construction
reuse.weights.matrix

Can be used in conjunction with the store.weights parameter in TransferData to reuse a precomputed weights matrix.

Details

The main steps of this procedure are identical to IntegrateData 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 IntegrateData.

Value

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.

Seurat

Tools for Single Cell Genomics

v4.0.1
GPL-3 | file LICENSE
Authors
Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]
Initial release
2021-03-17

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