Run dimension reduction

Usage

RunDimsReduction(
  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: Features to plot.
assay: Assay to use. NULL uses the default assay.
layer: Assay layer to use.
linear_reduction: Linear reduction ("pca", "svd", "ica", "nmf", "mds", "glmpca"). linear_reduction_dims_use = NULL uses estimated dimensions, else the first 50.
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: Nonlinear reduction ("umap", "umap-naive", "tsne", "dm", "phate", "pacmap", "trimap", "largevis", "fr").
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: Optional integer seed. When supplied, every input receives a deterministic independent L'Ecuyer-CMRG random-number stream, making results reproducible across worker counts and scheduling order. The caller's random number state is restored when the call finishes.

Run dimension reduction

Usage

Arguments

See also