DetermineClusters: Perform clustering diagnostics

In jrSiCKLSNMF: Multimodal Single-Cell Omics Dimensionality Reduction

Perform clustering diagnostics

Description

A wrapper for the clValid and fviz_nbclust functions to perform clustering diagnostics

Usage

DetermineClusters(
  SickleJr,
  numclusts = 2:20,
  clusteringmethod = "kmeans",
  diagnosticmethods = c("wss", "silhouette", "gap_stat"),
  clValidvalidation = "internal",
  createDiagnosticplots = TRUE,
  runclValidDiagnostics = TRUE,
  printPlots = TRUE,
  printclValid = TRUE,
  subset = FALSE,
  subsetsize = 1000,
  seed = NULL
)

Arguments

SickleJr	An object of class SickleJr
numclusts	A vector of integers indicating the number of clusters to test
clusteringmethod	String holding the clustering method: defaults to k-means; since the other methods are not implemented in jrSiCKLSNMF, it is recommended to use k-means.
diagnosticmethods	Vector of strings indicating which methods to plot. Defaults to all three of the available: wss, silhouette, and gap_stat
clValidvalidation	String containing validation method to use for clValid. Defaults to internal.
createDiagnosticplots	Boolean indicating whether to create diagnostic plots for cluster size
runclValidDiagnostics	Boolean indicating whether to calculate the diagnostics from clValid
printPlots	Boolean indicating whether to print the diagnostic plots
printclValid	Boolean indicating whether to print the diagnostic results from clValid
subset	Boolean indicating whether to calculate the diagnostics on a subset of the data rather than on the whole dataset.
subsetsize	Numeric value indicating size of the subset
seed	Numeric value holding the random seed

Value

An object of class SickleJr with cluster diagnostics added to its clusterdiagnostics slot

References

\insertRef

clValidjrSiCKLSNMF

\insertRef

factoextrajrSiCKLSNMF

Examples

#Since these data are too small, the clValid diagnostics do not run
#properly. See the vignette for an example with the clValid diagnostics
SimSickleJrSmall<-DetermineClusters(SimSickleJrSmall,numclusts=2:5,runclValidDiagnostics=FALSE)

jrSiCKLSNMF documentation built on Aug. 12, 2025, 1:08 a.m.