SilhouetteCurve {ILoReg} | R Documentation

## 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)

[Package ILoReg version 1.0.0 Index]