silhouettePlot: Plot silhouette plot to evaluate classification

In jsemple19/EMclassifieR: Classify DSMF data using the Expectation Maximisation algorithm

Plot silhouette plot to evaluate classification

Description

Create a silhouette plot to evaluate the quality of classification, and return some basic parameters about the classification

Usage

silhouettePlot(
  dataOrderedByClass,
  numClasses,
  outFileBase,
  EMrep = NULL,
  distMetric = list(name = "euclidean", rescale = F)
)

Arguments

dataOrderedByClass	A matrix of methylation or bincount values (reads x position) that have been ordered by class. The assigned class, e.g. "__class1" etc has been appended to read names.
numClasses	An integer with the number of classes learned
outFileBase	A string that will be used in the filenames and titles of the plots produced
EMrep	An integer indicating which EM repeat this is
distMetric	A list with the name of the distance metric and any parameters it might require

Value

A list of two items: a dataframe with silhouette stats and a silhouette plot object. The dataframe contains mean and SD of silhouette width overall, and per class, as well as number of reads per class

jsemple19/EMclassifieR documentation built on Aug. 12, 2022, 2:57 p.m.