plot_silhouette: Generates a silhouette plot for a given clustering...

In cbg-ethz/TMixClust: Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines

Description

plot_silhouette

Usage

plot_silhouette(TMixClust_object, sim_metric = "euclidean",
  sil_color = "#bdbdbd")

Arguments

TMixClust_object	list object created by the TMixClust function (see function TMixClust)
sim_metric	character string taking one of the possible values: "euclidean", "gower" or "manhattan". Default is "euclidean".
sil_color	color of the bars representing the silhouette widths on the plot

Value

List object with the following components:

• similarity_m similarity matrix

• silh silhouette object

Renders a plot comprised of a set of barplots with the distributions of silhouette coefficients for the data points in each cluster. Each barplot has indicated on its right hand side the total number of points in the corresponding cluster. The plot also indicates with a dotted line, the overall average silhouette width, whose value is specified at the bottom of the plot.

Author(s)

Monica Golumbeanu, [e-mail]

References

Golumbeanu M, Desfarges S, Hernandez C, Quadroni M, Rato S, Mohammadi P, Telenti A, Beerenwinkel N, Ciuffi A. (2017) Dynamics of Proteo-Transcriptomic Response to HIV-1 Infection.

Examples

# Load the TMixClust object associated to the toy time series data
# provided with the TMixClust package
data(best_clust_toy_obj)

# Plot the silhouette for the clustering stored in the toy TMixClust object
plot_silhouette(best_clust_toy_obj)

cbg-ethz/TMixClust documentation built on May 30, 2019, 8:28 a.m.