LocalStruct: Calculate the local structure preservation metric

In satijalab/seurat: Tools for Single Cell Genomics

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

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.