Seurat: LocalStruct – R documentation

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LocalStruct

Calculate the local structure preservation metric

Description

Calculates a metric that describes how well the local structure of each group prior to integration is preserved after integration. This procedure works as follows: For each group, compute a PCA, compute the top num.neighbors in pca space, compute the top num.neighbors in corrected pca space, compute the size of the intersection of those two sets of neighbors. Return the average over all groups.

Usage

LocalStruct(
  object,
  grouping.var,
  idents = NULL,
  neighbors = 100,
  reduction = "pca",
  reduced.dims = 1:10,
  orig.dims = 1:10,
  verbose = TRUE
)

Arguments

`object`	Seurat object
`grouping.var`	Grouping variable
`idents`	Optionally specify a set of idents to compute metric for
`neighbors`	Number of neighbors to compute in pca/corrected pca space
`reduction`	Dimensional reduction to use for corrected space
`reduced.dims`	Number of reduced dimensions to use
`orig.dims`	Number of PCs to use in original space
`verbose`	Display progress bar

Value

Returns the average preservation metric

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