kingTetrahedron: 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")

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. More information (and links to the actual viewers) can be found at https://en.wikipedia.org/wiki/Kinemage

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

Author

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

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 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, more information (and links to the software) can be found at https://en.wikipedia.org/wiki/Kinemage. For this one has to put king=FALSE as a parameter.

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

Examples

Run this code

if (FALSE) {
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.
}

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