mclust3D: mclust Analysis in 3D

Description

This function conducts an mclust analysis of the data provided, and plots the points in 3D using rgl graphics. An option is provided for displaying either classical or robust confidence ellipses. An internal function not generally called by the user. See mclust3dSpectra instead.

Usage

mclust3D(data, ellipse = TRUE, rob = FALSE, cl = 0.95,
  frac.pts.used = 0.8, truth = NULL, title = "no title provided",
  t.pos = NULL, lab.opts = FALSE, use.sym = FALSE, ...)

Arguments

data

A matrix of 3 columns (corresponding to x, y, z) and samples in rows.

ellipse

Logical indicating if confidence ellipses should be drawn.

rob

Logical; if ellipse = TRUE, indicates that robust confidence ellipses should be drawn. If FALSE, classical confidence ellipses are drawn.

A number indicating the confidence interval for the ellipse.

frac.pts.used

If ellipse = TRUE and rob = TRUE, a number indicating the fraction of the data points to be considered "good" and thus used to compute the robust confidence ellipse.

truth

A character vector indicating the known group membership for reach row of the PC scores. Generally this would be spectra$groups.

title

A character string for the plot title.

t.pos

A character selection from LETTERS[1:8] ( = A through H) indicating the desired location for the title.

lab.opts

A logical indicating whether or not to display the locations where the title and legend can be placed. These locations are the corners of a cube surrounding the data.

use.sym

logical; if true, the color scheme is changed to black and symbols are used for plotting.

…

Other parameters to be passed downstream.

Value

The mclust model is returned invisibly, and a plot is produced.

References

https://github.com/bryanhanson/ChemoSpec

Examples

Run this code

# NOT RUN {
# }
# NOT RUN {
require("mclust")
set.seed(666)
x <- c(rnorm(10, 3, 0.5), rnorm(10, -1, 0.5))
y <- c(rnorm(10, 1, 1), rnorm(10, -4, 0.5))
z <- c(rnorm(10, -2, 0.5), rnorm(10, 3, 0.5))
x[15] <- y[15] <- z[15] <- 4 # screw up one point
my.truth <- c(rep("Z", 10), rep("Q", 10))
mclust3D(cbind(x, y, z), title = "mclust3D demo",
	 t.pos = "G", truth = my.truth)
# }
# NOT RUN {
# }