seuratElbowPlot {singleCellTK} | R Documentation

## seuratElbowPlot Computes the plot object for elbow plot from the pca slot in the input sce object

### Description

seuratElbowPlot Computes the plot object for elbow plot from the pca slot in the input sce object

### Usage

    seuratElbowPlot(
      inSCE,
      significantPC = NULL,
      reduction = "pca",
      ndims = 20,
      externalReduction = NULL,
      interactive = TRUE
    )

### Arguments

`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 `NULL`, all points will be the same color. Default `NULL`.
`reduction` | Reduction to use for elbow plot generation. Either `"pca"` or `"ica"`. Default `"pca"`.
`ndims` | Number of components to use. Default `20`.
`externalReduction` | Pass DimReduc object if PCA/ICA computed through other libraries. Default `NULL`.
`interactive` | 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`.

### Value

plot object

### Examples

    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)

[Package singleCellTK version 2.2.0 Index]