PCAElbowPlot: Elbow plot of the standard deviations of the principal...

In elolab/iloreg: ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data

Elbow plot of the standard deviations of the principal components

Description

Draw an elbow plot of the standard deviations of the principal components to deduce an appropriate value for p.

Usage

PCAElbowPlot.SingleCellExperiment(object, return.plot)

## S4 method for signature 'SingleCellExperiment'
PCAElbowPlot(object, return.plot = FALSE)

Arguments

object	object of class 'iloreg'
return.plot	logical indicating if the ggplot2 object should be returned (default FALSE)

Value

ggplot2 object if return.plot=TRUE

Examples

library(SingleCellExperiment)
sce <- SingleCellExperiment(assays = list(logcounts = pbmc3k_500))
sce <- PrepareILoReg(sce)
## These settings are just to accelerate the example, use the defaults.
sce <- RunParallelICP(sce,L=2,threads=1,C=0.1,k=5,r=1)
sce <- RunPCA(sce,p=5)
PCAElbowPlot(sce)

elolab/iloreg documentation built on March 27, 2022, 4:19 a.m.