bulkUMAP {MOCHA}

bulkUMAP

Description

bulkUMAP generates UMAP from pseudobulk LSIObj object, and merges in metadata.

Usage

bulkUMAP(
  SEObj,
  assay = "LSI",
  components = c(1:30),
  nNeighbors = 15,
  returnModel = FALSE,
  seed = 1,
  ...
)

Arguments

SEObj

The SummarizedExperiment object output from bulkDimReduction, or an STM, subsetted down to just one cell type.

assay

A string, describing the name of the assay within SEObj to run UMAP ('PCA', 'LSI', or 'counts').

components

A vector of integers. Number of components to include in LSI (1:30 typically).

nNeighbors

See umap. The size of local neighborhood (in terms of number of neighboring sample points) used for manifold approximation. Default is 15.

returnModel

A boolean. Default is FALSE. If set to true, it will return a list, where the first is the UMAP coordinates with metadata for plotting, and the second is the full UMAP model so further projection can occur.

seed

an integer. Represents the random seed to pass to the UMAP. Default seed is 1.

...

Additional arguments to be passed to umap.

Value

fullUMAP data.frame of UMAP values with metadata attached.

Examples

## Not run: 
UMAPvalues <- MOCHA::bulkUMAP(LSIObj)

## End(Not run)