plot3dacomp: 3D-plot of compositional data

In compositions: Compositional Data Analysis

3D-plot of compositional data

Description

3D-plot of compositional data. The plot is mainly an exploratory tool, not intended for exact display of data.

Usage

 ## S3 method for class 'acomp'
plot3D(x, parts=1:min(ncol(X),4),..., 
             lwd=2, axis.col="gray", add=FALSE, cex=2, 
             vlabs=colnames(x), vlabs.col=axis.col, center=FALSE, 
             scale=FALSE, log=FALSE, bbox=FALSE, axes=TRUE, size=cex,col=1)
## S3 method for class 'rcomp'
plot3D(x,parts=1:min(ncol(X),4),...,
             lwd=2,axis.col="gray",add=FALSE,cex=2,
             vlabs=colnames(x),vlabs.col=axis.col,center=FALSE,
             scale=FALSE,log=FALSE,bbox=FALSE,axes=TRUE,size=cex,col=1)

Arguments

x	an aplus object to be plotted
parts	a numeric xor character vector of length 3 coding the columns to be plotted
...	additional plotting parameters as described in rgl::material3d
add	logical, adding or new plot
cex	size of the plotting symbols
lwd	line width
axis.col	color of the axis
vlabs	the column names to be plotted, if missing defaults to the column names of the selected columns of X
vlabs.col	color of the labels
center	logical, should the data be centered
scale	logical, should the data be scaled
log	logical, indicating wether to plot in log scale
bbox	logical, whether to add a bounding box
axes	logical, whether plot a coordinate cross
size	size of the plotting symbols
col	the color used for dots, defaults to black.

Details

The routine behaves different when 3 or four components should be plotted. In case of four components:
If log is TRUE the data is plotted in ilr coordinates. This is the isometric view of the data.
If log is FALSE the data is plotted in ipt coordinates and a tetrahedron is plotted around it if coors == TRUE. This can be used to do a tetrahedron plot.
In case of three components:
If log is TRUE the data is plotted in clr coordinates. This can be used to visualize the clr plane.
If log is FALSE the data is plotted as is, showing the embedding of the three-part simplex in the three-dimensional space.
In all cases: If coors is true, coordinate arrows are plotted of length 1 in the origin of the space, except in the tetrahedron case.

Value

Called for its side effect of a 3D plot of an acomp object in an rgl plot. It invisibly returns the 3D plotting coordinates of the objects displayed

Note

The function kingTetrahedron provides an alternate way of tetrahedron plots, based on a more advanced viewer, which must be downloaded separately.

Author(s)

K.Gerald v.d. Boogaart http://www.stat.boogaart.de

See Also

kingTetrahedron rgl::points3d, graphics::plot, plot3D, plot3D.rmult,

plot3D.rcomp, plot3D.aplus,plot3D.rplus

Examples

data(SimulatedAmounts)
if(requireNamespace("rgl", quietly = TRUE)) {
  plot3D(acomp(sa.lognormals5),1:3,col="green")
  plot3D(acomp(sa.lognormals5),1:3,log=TRUE,col="green")
  plot3D(acomp(sa.lognormals5),1:4,col="green")
  plot3D(acomp(sa.lognormals5),1:4,log=TRUE,col="green")
} ## this function requires package 'rgl'

compositions documentation built on June 22, 2024, 12:15 p.m.