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

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

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)

ILoReg documentation built on Nov. 8, 2020, 8:20 p.m.