R/seuratFunctions.R
seuratElbowPlot.Rd
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") if (FALSE) { sce <- seuratNormalizeData(sce, useAssay = "counts") sce <- seuratFindHVG(sce, useAssay = "counts") sce <- seuratScaleData(sce, useAssay = "counts") sce <- seuratPCA(sce, useAssay = "counts") seuratElbowPlot(sce) }