Run UMAP — run_umap • scooter

The default method runs uwot::umap2() on a matrix; the Seurat method runs Seurat::RunUMAP() with umap.method = "uwot2" (also uwot::umap2()) and stores a "umap<suffix>" reduction. Defaults match Seurat::RunUMAP() (30 neighbors, minimum distance 0.3) rather than the lower uwot defaults.

Usage

run_umap(x, ...)

# Default S3 method
run_umap(x, num_neighbors = 30, min_dist = 0.3, suffix = "", ...)

# S3 method for class 'Seurat'
run_umap(
  x,
  num_neighbors = 30,
  min_dist = 0.3,
  suffix = "",
  assay = "RNA",
  reduction = NULL,
  num_dim = NULL,
  features = NULL,
  var_features = FALSE,
  graph = NULL,
  file_format = c("png", "pdf"),
  ...
)

Arguments

x: A matrix (default) or a Seurat object.
...: Passed to the underlying function.
num_neighbors: Number of neighbors.
min_dist: Minimum distance between points in the embedding.
suffix: Tag inserted into the reduction/column names.
assay: Assay to use (Seurat method). Always set explicitly.
reduction: Existing reduction to take dimensions from (Seurat method).
num_dim: Number of dimensions to take from reduction (Seurat method).
features: Explicit features to use (Seurat method).
var_features: Use the assay's variable features (Seurat method).
graph: Graph to use as input (Seurat method).
file_format: File formats to write the scatter plot in (Seurat method).

Value

A UMAP embedding matrix (default) or a Seurat object with the reduction added. The Seurat method also writes a sample-colored scatter of the result to the working directory, as dr.<reduction>.png/.pdf (or just .png if file_format = "png").