plotUMAP | R Documentation |
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"
)
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" |
a UMAP plot of the reduced dimensions.
data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runQuickUMAP(sce)
plotUMAP(sce)
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