CalcSilhouette: Calculates silhouette widths for all cells in sCVdata

In BaderLab/scClustViz: Differential Expression-based scRNAseq Cluster Assessment and Viewing

Calculates silhouette widths for all cells in sCVdata

Description

Calls silhouette to calculate silhouette widths (a metric indicating each cell's contribution to cluster cohesion / separation) for all cells in the sCVdata object, using the cell embedding used in clustering (see Param(sCVd,"DRforClust")).

Usage

CalcSilhouette(sCVd, inD)

## S4 method for signature 'sCVdata'
CalcSilhouette(sCVd, inD)

Arguments

sCVd	An sCVdata object.
inD	The input dataset. An object of class seurat or SingleCellExperiment. Other data classes are not currently supported. Please submit requests for other data objects here!

Value

A silhouette object containing the silhouette widths for all cells in the sCVdata object.

Methods (by class)

• sCVdata: Calculate silhouette widths for sCVdata

See Also

CalcSCV for wrapper function to calculate all statistics for an sCVdata object, fx_calcSilhouette for the internal function this method points to, and silhouette for the function doing the calculations.

Examples

## Not run: 
Silhouette(your_sCV_obj) <- CalcSilhouette(sCVd=your_sCV_obj,
                                           inD=your_scRNAseq_data_object)

## End(Not run)

BaderLab/scClustViz documentation built on Sept. 10, 2023, 11:51 p.m.