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,
  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.

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") }