Dimensional Reduction

Run PCA, TSNE and UMAP on a seurat object perplexity should not be bigger than 3 * perplexity < nrow(X) - 1, see details for interpretation

seurat_reduce_dimensions(
  seu,
  assay = "gene",
  reduction = "pca",
  legacy_settings = FALSE,
  ...
)

Arguments

seu

A Seurat object

assay

Assay of interest to be run on the seurat object

reduction

Set dimensional reduction object

legacy_settings

Use legacy settings

...

Extra parameters passed to seurat_reduce_dimensions