RunDimReduction: Run dimensionality reduction
In zh542370159/SCP: Single Cell Pipeline

RunDimReduction

R Documentation

Run dimensionality reduction

Description

Run dimensionality reduction

Usage

RunDimReduction(
  srt,
  prefix = "",
  features = NULL,
  assay = NULL,
  slot = "data",
  linear_reduction = NULL,
  linear_reduction_dims = 50,
  linear_reduction_params = list(),
  force_linear_reduction = FALSE,
  nonlinear_reduction = NULL,
  nonlinear_reduction_dims = 2,
  reduction_use = NULL,
  reduction_dims = NULL,
  graph_use = NULL,
  neighbor_use = NULL,
  nonlinear_reduction_params = list(),
  force_nonlinear_reduction = TRUE,
  verbose = TRUE,
  seed = 11
)

Arguments

`srt`	A Seurat object.
`prefix`	The prefix used to name the result.
`features`	Use features expression data to run linear or nonlinear dimensionality reduction.
`assay`	Specific assay to get data from.
`slot`	Specific slot to get data from.
`linear_reduction`	Method of linear dimensionality reduction. Options are "pca", "ica", "nmf", "mds", "glmpca".
`linear_reduction_dims`	Total number of dimensions to compute and store for `linear_reduction`.
`linear_reduction_params`	Other parameters passed to the `linear_reduction` method.
`force_linear_reduction`	Whether force to do linear dimensionality reduction.
`nonlinear_reduction`	Method of nonlinear dimensionality reduction. Options are "umap", "umap-naive", "tsne", "dm", "phate", "pacmap", "trimap", "largevis"
`nonlinear_reduction_dims`	Total number of dimensions to compute and store for `nonlinear_reduction`.
`reduction_use`	Which dimensional reduction to use as input for `nonlinear_reduction`.
`reduction_dims`	Which dimensions to use as input for `nonlinear_reduction`, used only if `features` is `NULL`.
`graph_use`	Name of graph to use for the `nonlinear_reduction`.
`neighbor_use`	Name of neighbor to use for the `nonlinear_reduction`.
`nonlinear_reduction_params`	Other parameters passed to the `nonlinear_reduction` method.
`force_nonlinear_reduction`	Whether force to do nonlinear dimensionality reduction.
`verbose`	Show messages.
`seed`	Set a seed.