seuratRunUMAP {singleCellTK} | R Documentation |
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 )
inSCE |
(sce) object on which to compute the UMAP |
useReduction |
Reduction to use for computing UMAP. One of "pca" or
"ica". Default is |
reducedDimName |
Name of new reducedDims object containing Seurat UMAP
Default |
dims |
Numerical value of how many reduction components to use for UMAP
computation. Default |
minDist |
Sets the |
nNeighbors |
Sets the |
spread |
Sets the |
verbose |
Logical value indicating if informative messages should
be displayed. Default is |
Updated sce object with UMAP computations stored
data(scExample, package = "singleCellTK") ## Not run: 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") ## End(Not run)