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Last data update: 2014.03.03

R: Displays a Linkage Map

LinkageMap

R Documentation

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] < 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

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