plotSeuratJackStraw: plotSeuratJackStraw Computes the plot object for jackstraw...

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

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

Description

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

Usage

plotSeuratJackStraw(
  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 <- runSeuratNormalizeData(sce, useAssay = "counts")
sce <- runSeuratFindHVG(sce, useAssay = "counts")
sce <- runSeuratScaleData(sce, useAssay = "counts")
sce <- runSeuratPCA(sce, useAssay = "counts")
sce <- runSeuratJackStraw(sce, useAssay = "counts")
plotSeuratJackStraw(sce)

## End(Not run)

compbiomed/singleCellTK documentation built on Feb. 10, 2024, 3:32 a.m.