Generate UMAP from pseudobulk LSI results

bulkUMAP generates UMAP from pseudobulk LSIObj object from bulkDimReduction

Usage

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

SEObj: The SummarizedExperiment object output from bulkDimReduction, or an STM, subset 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.

fullUMAP data.frame of UMAP values with metadata attached.

if (FALSE) {
UMAPvalues <- MOCHA::bulkUMAP(LSIObj)
}