DoUMAP

Perform UMAP dimentional reduction

DoUMAP(
  object,
  reduction_use = "pca",
  reduction_save = "umap",
  dims_use = NULL,
  ...
)

Arguments

object

A Seurat or SingleCellExperiment object to be transformed.

reduction_use

Prior dimensional reduction to use for calculations (i.e. pca, ica, cca, etc...). Default: pca

reduction_save

Name to use for the reduction (i. e. tsne, umap, etc...). Default: umap

dims_use

Dimensions from `reduction_use` to pass to PHATE

...

Extra parameters to pass to the umap function.