R/plotUMAP.R
plotUMAP.Rd
Plot UMAP results either on already run results or run first and then plot.
plotUMAP(
inSCE,
colorBy = "No Color",
shape = "No Shape",
reducedDimName = "UMAP",
runUMAP = FALSE,
useAssay = "logcounts"
)
Input SingleCellExperiment object with saved dimension reduction components. Required
color by a condition(any column of the annotation data).
add shapes to each condition.
saved dimension reduction name in the SingleCellExperiment object. Required.
If the dimension reduction components are already available set this to FALSE, otherwise set to TRUE. Default is False.
Indicate which assay to use. The default is "logcounts"
a UMAP plot of the reduced dimensions.
data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- getUMAP(inSCE = sce, useAssay = "counts", reducedDimName = "UMAP")
#> 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, shape = "No Shape", reducedDimName = "UMAP",
runUMAP = TRUE, useAssay = "counts")