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