seuratElbowPlot {singleCellTK} | R Documentation |
seuratElbowPlot Computes the plot object for elbow plot from the pca slot in the input sce object
seuratElbowPlot( inSCE, significantPC = NULL, reduction = "pca", ndims = 20, externalReduction = NULL, interactive = TRUE )
inSCE |
(sce) object from which to compute the elbow plot (pca should be computed) |
significantPC |
Number of significant principal components to plot.
This is used to alter the color of the points for the corresponding PCs.
If |
reduction |
Reduction to use for elbow plot generation. Either
|
ndims |
Number of components to use. Default |
externalReduction |
Pass DimReduc object if PCA/ICA computed through
other libraries. Default |
interactive |
Logical value indicating if the returned object should
be an interactive plotly object if |
plot object
data(scExample, package = "singleCellTK") ## Not run: sce <- seuratNormalizeData(sce, useAssay = "counts") sce <- seuratFindHVG(sce, useAssay = "counts") sce <- seuratScaleData(sce, useAssay = "counts") sce <- seuratPCA(sce, useAssay = "counts") seuratElbowPlot(sce) ## End(Not run)