# LinkageMap: Displays a Linkage Map In VisuClust: Visualisation of Clusters in Multivariate Data

## 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] < d[i,j] <= t[k] The ranges can be changed dynamically at runtime by changing the thresholds t[k] with sliders.

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

 ```1 2 3 4``` ```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).

## Author(s)

Michael Sieger <sieger-michael@web.de>
Georg Ohmayer <georg.ohmayer@hswt.de>

## Examples

 ```1 2 3 4 5 6 7 8 9``` ```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]) ```

VisuClust documentation built on May 2, 2019, 6:53 a.m.