seuratJackStrawPlot {singleCellTK} | R Documentation

## seuratJackStrawPlot Computes the plot object for jackstraw plot from the pca slot in the input sce object

### Description

seuratJackStrawPlot Computes the plot object for jackstraw plot from the pca slot in the input sce object

### Usage

    seuratJackStrawPlot(
      inSCE,
      dims = NULL,
      xmax = 0.1,
      ymax = 0.3,
      externalReduction = NULL
    )

### Arguments

`inSCE` | (sce) object from which to compute the jackstraw plot (pca should be computed)
`dims` | Number of components to plot in Jackstraw. If `NULL`, then all components are plotted Default `NULL`.
`xmax` | X-axis maximum on each QQ plot. Default `0.1`.
`ymax` | Y-axis maximum on each QQ plot. Default `0.3`.
`externalReduction` | Pass DimReduc object if PCA/ICA computed through other libraries. Default `NULL`.

### 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")
    sce <- seuratComputeJackStraw(sce, useAssay = "counts")
    seuratJackStrawPlot(sce)

    ## End(Not run)

[Package singleCellTK version 2.2.0 Index]