Run UMAP on CHOIR dimensionality reductions

Simplifies running Seurat::RunUMAP() after CHOIR clustering by automatically fetching the pre-generated dimensionality reductions.

Usage

runCHOIRumap(object, key = "CHOIR", reduction = NULL, verbose = TRUE)

Arguments

object

An object of class Seurat, SingleCellExperiment, or ArchRProject that has undergone CHOIR clustering. For multi-omic data, we recommend using ArchRProject objects.

key

The name under which CHOIR-related data for this run is stored in the object. Defaults to “CHOIR”.

reduction

A character vector indicating which CHOIR subtree dimensionality reduction to run UMAP on (e.g., 'P0_reduction', 'P1_reduction'). Default = NULL will run UMAP on all of the dimensionality reductions generated by CHOIR stored under the provided key.

verbose

A Boolean value indicating whether to use verbose output during the execution of CHOIR. Defaults to TRUE, but can be set to FALSE for a cleaner output.

Value

Returns the object with the following added data stored under the provided key:

reduction

Cell embeddings for all calculated dimensionality reductions