R/seuratFunctions.R
plotSeuratReduction.Rd
plotSeuratReduction Plots the selected dimensionality reduction method
plotSeuratReduction(
inSCE,
useReduction = c("pca", "ica", "tsne", "umap"),
showLegend = FALSE,
groupBy = NULL,
splitBy = NULL
)
(sce) object which has the selected dimensionality reduction algorithm already computed and stored
Dimentionality reduction to plot. One of "pca", "ica",
"tsne", or "umap". Default "umap"
.
Select if legends and labels should be shown on the output
plot or not. Either "TRUE" or "FALSE". Default FALSE
.
Specify a colData column name that be used for grouping.
Default is NULL
.
Specify a colData column name that be used for splitting the
output plot. Default is NULL
.
plot object
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")
plotSeuratReduction(sce, useReductionPlot = "pca")}