R/seuratFunctions.R
plotSeuratElbow.Rd
plotSeuratElbow Computes the plot object for elbow plot from the pca slot in the input sce object
plotSeuratElbow(
inSCE,
significantPC = NULL,
reduction = "pca",
ndims = 20,
externalReduction = NULL,
interactive = TRUE
)
(sce) object from which to compute the elbow plot (pca should be computed)
Number of significant principal components to plot.
This is used to alter the color of the points for the corresponding PCs.
If NULL
, all points will be the same color. Default NULL
.
Reduction to use for elbow plot generation. Either
"pca"
or "ica"
. Default "pca"
.
Number of components to use. Default 20
.
Pass DimReduc object if PCA/ICA computed through
other libraries. Default NULL
.
Logical value indicating if the returned object should
be an interactive plotly object if TRUE
or a ggplot object if
set to FALSE
. Default is TRUE
.
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")
plotSeuratElbow(sce)
}