Run dimension reduction

Usage

RunDimReduction(
  srt,
  prefix = "",
  features = NULL,
  assay = NULL,
  layer = "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: A character vector of features to use. Default is NULL.
assay: Which assay to use. If NULL, the default assay of the Seurat object will be used.
layer: Which layer to use. Default is "counts".
linear_reduction: The linear dimensionality reduction method to use. Options are "pca", "svd", "ica", "nmf", "mds", or "glmpca". Default is "pca".
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 dimension reduction.
nonlinear_reduction: The nonlinear dimensionality reduction method to use. Options are "umap", "umap-naive", "tsne", "dm", "phate", "pacmap", "trimap", "largevis", or "fr". Default is "umap".
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 dimension reduction.
verbose: Whether to print the message. Default is TRUE.
seed: Random seed for reproducibility. Default is 11.

Run dimension reduction

Usage

Arguments

See also