R: Ploting composition into rotable tetrahedron

kingTetrahedron {compositions} | R Documentation

## Ploting composition into rotable tetrahedron

### Description

Plots acomp/rcomp objects into tetrahedron exported in kinemage format.

### Usage

       kingTetrahedron(X, parts=1:4, file="tmptetrahedron.kin",
       clu=NULL,vec=NULL, king=TRUE, scale=0.2, col=1,
       title="Compositional Tetrahedron")

### Arguments

`X` | a compositional acomp or rcomp object of 4 or more parts
`parts` | a numeric or character vector specifying the 4 parts to be used.
`file` | file.kin for 3D display with the KiNG (Kinemage, Next Generation) interactive system for three-dimensional vector graphics.
`clu` | partition determining the colors of points
`vec` | vector of values determining points sizes
`king` | FALSE for Mage; TRUE for King (described below)
`scale` | relative size of points
`col` | color of points if clu=NULL
`title` | The title of the plot

### Details

The routine transforms a 4 parts mixture m quadrays into 3-dimensional XYZ coordinates and writes them as file.kin. For this transformation we apply K. Urner: Quadrays and XYZ at http://www.grunch.net/synergetics/quadxyz.html. The kin file we display as 3-D animation with KiNG viewer a free software available at http://kinemage.biochem.duke.edu. A kinemage is a dynamic, 3-D illustration. The best way to take advantage of that is by rotating it and twisting it around with the mouse click near the center of the graphics window and slowly draging right or left, up or down. Furthermore by clicking on points with the mouse (left button again), the label associated with each point will appear in the bottom left of the graphics area and also the distance from this point to the last will be displayed. With the right button drag we can zoom in and out of the picture. This animation supports coloring and different sizing of points.

We can display the kin file as 3-D animation also with MAGE viewer a previous version of KiNG, also a free software available at http://kinemage.biochem.duke.edu. For this one has to put king=FALSE as a parameter.

### Value

The function is called for its side effect of generating a file for 3D display with the KiNG (Kinemage, Next Generation) interactive system for three-dimensional vector graphics. Works only with KiNG viewer available at http://kinemage.biochem.duke.edu

### Note

This routine and the documentation is based on mix.Quad2net from the MixeR-package of Vladimir Batagelj and Matevz Bren, and has been contributed by Matevz Bren to this package. Only slight modifications have been applied to make function compatible with the philosophy and objects of the compositions package.

### Author(s)

Vladimir Batagelj and Matevz Bren, with slight modifications of K.Gerald van den Boogaart

### References

Aitchison, J. (1986) The Statistical Analysis of Compositional Data Monographs on Statistics and Applied Probability. Chapman & Hall Ltd., London (UK). 416p.

http://vlado.fmf.uni-lj.si/pub/MixeR/

http://www.grunch.net/synergetics/quadxyz.html

### See Also

`plot.acomp`

### Examples

    data(SimulatedAmounts)
    dat <- acomp(sa.groups5)
    hc <- hclust(dist(dat), method = "complete")  # data are clustered
    kingTetrahedron(dat,parts=1:4, file="myfirst.kin", clu=cutree(hc,7),
    scale=0.2)
    # the 3-D plot is written into Glac1.kin file to be displayed with KiNG viewer.
    # The seven clusters partition is notated with different colors of points.

[Package compositions version 1.40-2 Index]