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

seuratRunUMAP(
  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 <- seuratNormalizeData(sce, useAssay = "counts")
sce <- seuratFindHVG(sce, useAssay = "counts")
sce <- seuratScaleData(sce, useAssay = "counts")
sce <- seuratPCA(sce, useAssay = "counts")
sce <- seuratFindClusters(sce, useAssay = "counts")
sce <- seuratRunUMAP(sce, useReduction = "pca")
}