mclust (version 5.3)

coordProj: Coordinate projections of multidimensional data modeled by an MVN mixture.

Description

Plots coordinate projections given multidimensional data and parameters of an MVN mixture model for the data.

Usage

coordProj(data, dimens = c(1,2), parameters = NULL, z = NULL,
          classification = NULL, truth = NULL, uncertainty = NULL, 
          what = c("classification", "errors", "uncertainty"),
          addEllipses = TRUE, symbols = NULL, colors = NULL, scale = FALSE, 
          xlim = NULL, ylim = NULL, CEX = 1, PCH = ".", main = FALSE, …)

Arguments

data

A numeric matrix or data frame of observations. Categorical variables are not allowed. If a matrix or data frame, rows correspond to observations and columns correspond to variables.

dimens

A vector of length 2 giving the integer dimensions of the desired coordinate projections. The default is c(1,2), in which the first dimension is plotted against the second.

parameters

A named list giving the parameters of an MCLUST model, used to produce superimposing ellipses on the plot. The relevant components are as follows:

mean

The mean for each component. If there is more than one component, this is a matrix whose kth column is the mean of the kth component of the mixture model.

variance

A list of variance parameters for the model. The components of this list depend on the model specification. See the help file for mclustVariance for details.

z

A matrix in which the [i,k]th entry gives the probability of observation i belonging to the kth class. Used to compute classification and uncertainty if those arguments aren't available.

classification

A numeric or character vector representing a classification of observations (rows) of data. If present argument z will be ignored.

truth

A numeric or character vector giving a known classification of each data point. If classification or z is also present, this is used for displaying classification errors.

uncertainty

A numeric vector of values in (0,1) giving the uncertainty of each data point. If present argument z will be ignored.

what

Choose from one of the following three options: "classification" (default), "errors", "uncertainty".

addEllipses

A logical indicating whether or not to add ellipses with axes corresponding to the within-cluster covariances in case of "classification" or "uncertainty" plots.

symbols

Either an integer or character vector assigning a plotting symbol to each unique class in classification. Elements in colors correspond to classes in order of appearance in the sequence of observations (the order used by the function unique). The default is given by mclust.options("classPlotSymbols").

colors

Either an integer or character vector assigning a color to each unique class in classification. Elements in colors correspond to classes in order of appearance in the sequence of observations (the order used by the function unique). The default is given by mclust.options("classPlotColors").

scale

A logical variable indicating whether or not the two chosen dimensions should be plotted on the same scale, and thus preserve the shape of the distribution. Default: scale=FALSE

xlim, ylim

Arguments specifying bounds for the ordinate, abscissa of the plot. This may be useful for when comparing plots.

CEX

An argument specifying the size of the plotting symbols. The default value is 1.

PCH

An argument specifying the symbol to be used when a classification has not been specified for the data. The default value is a small dot ".".

main

A logical variable or NULL indicating whether or not to add a title to the plot identifying the dimensions used.

…

Other graphics parameters.

Side Effects

A plot showing a two-dimensional coordinate projection of the data, together with the location of the mixture components, classification, uncertainty, and/or classification errors.

References

C. Fraley and A. E. Raftery (2002). Model-based clustering, discriminant analysis, and density estimation. Journal of the American Statistical Association 97:611-631.

C. Fraley, A. E. Raftery, T. B. Murphy and L. Scrucca (2012). mclust Version 4 for R: Normal Mixture Modeling for Model-Based Clustering, Classification, and Density Estimation. Technical Report No. 597, Department of Statistics, University of Washington.

See Also

clPairs, randProj, mclust2Dplot, mclust.options

Examples

# NOT RUN {
est <- meVVV(iris[,-5], unmap(iris[,5]))

# }
# NOT RUN {
par(pty = "s", mfrow = c(1,1))
coordProj(iris[,-5], dimens=c(2,3), parameters = est$parameters, z = est$z,
          what = "classification", main = TRUE) 
coordProj(iris[,-5], dimens=c(2,3), parameters = est$parameters, z = est$z,
          truth = iris[,5], what = "errors", main = TRUE) 
coordProj(iris[,-5], dimens=c(2,3), parameters = est$parameters, z = est$z,
          what = "uncertainty", main = TRUE) 
# }