RunGraphLaplacian: Run Graph Laplacian Eigendecomposition

In satijalab/seurat: Tools for Single Cell Genomics

Run Graph Laplacian Eigendecomposition

Description

Run a graph laplacian dimensionality reduction. It is used as a low dimensional representation for a cell-cell graph. The input graph should be symmetric

Usage

RunGraphLaplacian(object, ...)

## S3 method for class 'Seurat'
RunGraphLaplacian(
  object,
  graph,
  reduction.name = "lap",
  reduction.key = "LAP_",
  n = 50,
  verbose = TRUE,
  ...
)

## Default S3 method:
RunGraphLaplacian(object, n = 50, reduction.key = "LAP_", verbose = TRUE, ...)

Arguments

object	A Seurat object
...	Arguments passed to eigs_sym
graph	The name of graph
reduction.name	dimensional reduction name, lap by default
reduction.key	dimensional reduction key, specifies the string before the number for the dimension names. LAP by default
n	Total Number of Eigenvectors to compute and store (50 by default)
verbose	Print message and process

Value

Returns Seurat object with the Graph laplacian eigenvector calculation stored in the reductions slot

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