Plot UMAP results either on already run results or run first and then plot.

Plot UMAP results either on already run results or run first and then plot.

plotUMAP(
  inSCE,
  colorBy = NULL,
  shape = NULL,
  reducedDimName = "UMAP",
  runUMAP = FALSE,
  useAssay = "counts"
)

Arguments

inSCE

Input SingleCellExperiment object with saved dimension reduction components. Required

colorBy

color by a condition(any column of the annotation data).

shape

add shapes to each condition.

reducedDimName

saved dimension reduction name in the SingleCellExperiment object. Required.

runUMAP

If the dimension reduction components are already available set this to FALSE, otherwise set to TRUE. Default is False.

useAssay

Indicate which assay to use. The default is "logcounts"

Value

a UMAP plot of the reduced dimensions.

Examples

data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runQuickUMAP(sce)
#> Sat Mar 18 10:30:20 2023 ... Computing Scater UMAP for sample 'pbmc_4k'.
#> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by ‘spam’
#> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by ‘spam’
#> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by ‘spam’
plotUMAP(sce)