RunFR: Run Force-Directed Layout (Fruchterman-Reingold algorithm)

In zh542370159/SCP: Single Cell Pipeline

Run Force-Directed Layout (Fruchterman-Reingold algorithm)

Description

Run Force-Directed Layout (Fruchterman-Reingold algorithm)

Usage

RunFR(object, ...)

## S3 method for class 'Seurat'
RunFR(
  object,
  reduction = NULL,
  dims = NULL,
  features = NULL,
  assay = NULL,
  slot = "data",
  graph = NULL,
  neighbor = NULL,
  k.param = 20,
  ndim = 2,
  niter = 500,
  reduction.name = "FR",
  reduction.key = "FR_",
  verbose = TRUE,
  seed.use = 11L,
  ...
)

## Default S3 method:
RunFR(
  object,
  ndim = 2,
  niter = 500,
  reduction.key = "FR_",
  verbose = TRUE,
  seed.use = 11L,
  ...
)

Arguments

object	An object. This can be a Seurat object, a Neighbor object, or a Graph object.
...	Additional arguments to be passed to the layout_with_fr function.
reduction	A character string specifying the reduction to be used. Default is NULL.
dims	An integer vector specifying the dimensions to be used. Default is NULL.
features	A character vector specifying the features to be used. Default is NULL.
assay	A character string specifying the assay to be used. Default is NULL.
slot	A character string specifying the slot name to be used. Default is "data".
graph	A character string specifying the name of the Graph object to be used. Default is NULL.
neighbor	A character string specifying the name of the Neighbor object to be used. Default is NULL.
k.param	An integer specifying the number of nearest neighbors to consider. Default is 20.
ndim	An integer specifying the number of dimensions for the force-directed layout. Default is 2.
niter	An integer specifying the number of iterations for the force-directed layout. Default is 500.
reduction.name	A character string specifying the name of the reduction to be stored in the Seurat object. Default is "fr".
reduction.key	A character string specifying the prefix for the column names of the force-directed layout embeddings. Default is "FR_".
verbose	A logical value indicating whether to print verbose output. Default is TRUE.
seed.use	An integer specifying the random seed to be used. Default is 11.

Examples

pancreas_sub <- Seurat::FindVariableFeatures(pancreas_sub)
pancreas_sub <- RunFR(object = pancreas_sub, features = Seurat::VariableFeatures(pancreas_sub))
CellDimPlot(pancreas_sub, group.by = "CellType", reduction = "fr")

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.