Description Usage Arguments Author(s) Examples

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).

1 2 3 4 |

`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). |

Michael Sieger <sieger-michael@web.de>

Georg Ohmayer <georg.ohmayer@hswt.de>

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])
``` |

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