runSeuratUMAP Computes UMAP from the given sce object and stores the UMAP computations back into the sce object

runSeuratUMAP(
  inSCE,
  useReduction = c("pca", "ica"),
  reducedDimName = "seuratUMAP",
  dims = 10,
  minDist = 0.3,
  nNeighbors = 30L,
  spread = 1,
  externalReduction = NULL,
  seed = 42,
  verbose = TRUE
)

Arguments

inSCE: (sce) object on which to compute the UMAP
useReduction: Reduction to use for computing UMAP. One of "pca" or "ica". Default is "pca".
reducedDimName: Name of new reducedDims object containing Seurat UMAP Default seuratUMAP.
dims: Numerical value of how many reduction components to use for UMAP computation. Default 10.
minDist: Sets the "min.dist" parameter to the underlying UMAP call. See RunUMAP for more information. Default 0.3.
nNeighbors: Sets the "n.neighbors" parameter to the underlying UMAP call. See RunUMAP for more information. Default 30L.
spread: Sets the "spread" parameter to the underlying UMAP call. See RunUMAP for more information. Default 1.
externalReduction: Pass DimReduc object if PCA/ICA computed through other libraries. Default NULL.
seed: Random seed for reproducibility of results. Default 42.
verbose: Logical value indicating if informative messages should be displayed. Default is TRUE.

Value

Updated sce object with UMAP computations stored

Examples

data(scExample, package = "singleCellTK")
if (FALSE) {
sce <- runSeuratNormalizeData(sce, useAssay = "counts")
sce <- runSeuratFindHVG(sce, useAssay = "counts")
sce <- runSeuratScaleData(sce, useAssay = "counts")
sce <- runSeuratPCA(sce, useAssay = "counts")
sce <- runSeuratFindClusters(sce, useAssay = "counts")
sce <- runSeuratUMAP(sce, useReduction = "pca")
}