viewClusters: PLOT ALL CLUSTERS IN A 2-D PROJECTION SPACE

In clusterGeneration: Random Cluster Generation (with Specified Degree of Separation)

PLOT ALL CLUSTERS IN A 2-D PROJECTION SPACE

Description

Plot all clusters in a 2-D projection space.

Usage

viewClusters(
	     y, 
	     cl, 
	     outlierLabel = 0,
             projMethod = "Eigen", 
	     xlim = NULL, 
	     ylim = NULL,
             xlab = "1st projection direction", 
             ylab = "2nd projection direction", 
             title = "Scatter plot of 2-D Projected Clusters",
             font = 2, 
	     font.lab = 2, 
	     cex = 1.2, 
	     cex.lab = 1.2) 

Arguments

y	Data matrix. Rows correspond to observations. Columns correspond to variables.
cl	Cluster membership vector.
outlierLabel	Label for outliers. Outliers are not involved in calculating the projection directions. Outliers will be represented by red triangles in the plot. By default, outlierLabel=0.
projMethod	Method to construct 2-D projection directions. projMethod="Eigen" indicates that we project data to the 2-dimensional space spanned by the first two eigenvectors of the between cluster distance matrix B={2\over k_0}\sum_{i=1}^{k_0}\Sigma_i+{2\over k_0(k_0-1)}\sum_{i<j}(\theta_i-\theta_j) (\theta_i-\theta_j)^T. projMethod="DMS" indicates that we project data to the 2-dimensional space spanned by the first two eigenvectors of the between cluster distance matrix B=\sum_{i=2}^{k_0}\sum_{j=1}^{i-1} n_i n_j(\theta_i-\theta_j)(\theta_i-\theta_j)^T. “DMS” method is proposed by Dhillon et al. (2002).
xlim	Range of X axis.
ylim	Range of Y axis.
xlab	X axis label.
ylab	Y axis label.
title	Title of the plot.
font	An integer which specifies which font to use for text (see par).
font.lab	The font to be used for x and y labels (see par).
cex	A numerical value giving the amount by which plotting text and symbols should be scaled relative to the default (see par).
cex.lab	The magnification to be used for x and y labels relative to the current setting of 'cex' (see par).

Value

B	Between cluster distance matrix measuring the between cluster variation.
Q	Columns of Q are eigenvectors of the matrix B.
proj	Projected clusters in the 2-D space spanned by the first 2 columns of the matrix Q.

Author(s)

Weiliang Qiu [e-mail]
Harry Joe [e-mail]

References

Dhillon I. S., Modha, D. S. and Spangler, W. S. (2002) Class visualization of high-dimensional data with applications. computational Statistics and Data Analysis, 41, 59–90.

Qiu, W.-L. and Joe, H. (2006) Separation Index and Partial Membership for Clustering. Computational Statistics and Data Analysis, 50, 585–603.

See Also

plot1DProjection plot2DProjection

Examples

n1 <- 50
mu1 <- c(0, 0)
Sigma1 <- matrix(c(2, 1, 1, 5), 2, 2)
n2 <- 100
mu2 <- c(10, 0)
Sigma2 <- matrix(c(5, -1, -1, 2), 2, 2)
n3 <- 30
mu3 <- c(10, 10)
Sigma3 <- matrix(c(3, 1.5, 1.5, 1), 2, 2)
n4 <- 10
mu4 <- c(0, 0)
Sigma4 <- 50*diag(2)

library(MASS)
set.seed(1234)
y1 <- mvrnorm(n1, mu1, Sigma1)
y2 <- mvrnorm(n2, mu2, Sigma2)
y3 <- mvrnorm(n3, mu3, Sigma3)
y4 <- mvrnorm(n4, mu4, Sigma4)
y <- rbind(y1, y2, y3, y4)
cl <- rep(c(1:3, 0), c(n1, n2, n3, n4))

par(mfrow=c(2,1))
viewClusters(y = y, cl = cl)
viewClusters(y = y, cl = cl, projMethod = "DMS")

clusterGeneration documentation built on Aug. 16, 2023, 9:07 a.m.