VisuClust (version 1.2)

LinkageMap: Displays a Linkage Map

Description

A Linkage Map is a 2D Scatter Plot that displays the result of Sammon's Nonlinear Mapping. A number of ranges (>= 1) for the distance values d[i,j] can be defined. Each point pair whose distance is inside of the defined range is connected with a line.

The ranges are defined by thresholds t[k](1<=k<=3) in="" the="" following="" way="" range[1]:="" d[i,j]="" <="t[1]" range[k]:="" t[k-1]="" ranges="" can="" be="" changed="" dynamically="" at="" runtime="" by="" changing="" thresholds="" t[k]="" with="" sliders.="" p="">

A estimation of the density function for the distances d[i,j] (for example with kernel density estimation, see function density) is helpful for finding the ideal thresholds t[k] (=local minima in the density function).

Usage

LinkageMap(xSammon, dist, lineTypes=c("solid","dotted", "dashed"), 
	lineColors=c("red","green","blue"), lineWidths=c(1,1,1), 
	labels = NULL, cluster = NULL, maxValue=0.5, legendDigits = 2, 
	xlab = "", ylab = "", main = "")

Arguments

xSammon

A matrix with size (nPoints,2) that contains the projected points from Sammon's Nonlinear Mapping.

dist

A distance matrix for the given data (to compute with dist).

lineTypes

An array of line types. The size must match with line colors and line widths. The various line types are described in par.

lineColors

An array of colors. The size must match with line types and line widths. see colors

lineWidths

An array of line widths. The size must match with line colors and line types. see par

labels

A string-array with labels for the points (size: nPoints).

cluster

A array containing cluster memberships of the points. The point membership will be indicated with different colors. The array size must match with nPoints.

maxValue

maxValue*max(d[i,j]) is the maximum value that can be adjusted with the sliders.

legendDigits

The number of fractional digits to be displayed in the legend.

xlab

A title for the x axis (as described in plot).

ylab

A title for the y axis (as described in plot).

main

An overall title for the plot (as described in plot).

Examples

library(MASS)

data("MilchSmall")
M <- scale(MilchSmall[3:6])

D <- dist(M)
S <- sammon(D)
K <- kmeans(D,center=5)
LinkageMap(S$points, D, cluster=K$cluster, labels=MilchSmall[,2])