SilhouetteCurve: Silhouette curve

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

Silhouette curve

Description

Draw the silhouette curve: the average silhouette value across the cells for a range of different K values.

Usage

SilhouetteCurve.SingleCellExperiment(object, return.plot)

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

Arguments

object	of SingleCellExperiment class
return.plot	a logical denoting whether the ggplot2 object should be returned. Default is 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)
sce <- HierarchicalClustering(sce)
sce <- CalcSilhInfo(sce)
SilhouetteCurve(sce)

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