plot.MclustDA: Plotting method for MclustDA discriminant analysis

Description

Plots for model-based mixture discriminant analysis results, such as scatterplot of training and test data, classification of train and test data, and errors.

Usage

# S3 method for MclustDA
plot(x, what = c("scatterplot", "classification", "train&test", "error"), 
     newdata, newclass, dimens = NULL, 
     symbols, colors, main = NULL, ...)

Arguments

x

An object of class 'MclustDA' resulting from a call to MclustDA.

what

A string specifying the type of graph requested. Available choices are:

"scatterplot" =: a plot of training data with points marked based on the known classification. Ellipses corresponding to covariances of mixture components are also drawn.

"classification" =

a plot of data with points marked on based the predicted classification; if newdata is provided then the test set is shown otherwise the training set.

"train&test" =

a plot of training and test data with points marked according to the type of set.

"error" =

a plot of training set (or test set if newdata and newclass are provided) with misclassified points marked.

If not specified, in interactive sessions a menu of choices is proposed.

newdata

A data frame or matrix for test data.

newclass

A vector giving the class labels for the observations in the test data (if known).

dimens

A vector of integers giving the dimensions of the desired coordinate projections for multivariate data. The default is to take all the the available dimensions for plotting.

symbols

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

main

A logical, a character string, or NULL (default) for the main title. If NULL or FALSE no title is added to a plot. If TRUE a default title is added identifying the type of plot drawn. If a character string is provided, this is used for the title.

...

further arguments passed to or from other methods.

Author

Luca Scrucca

Details

For more flexibility in plotting, use mclust1Dplot, mclust2Dplot, surfacePlot, coordProj, or randProj.

Examples

Run this code

# \donttest{
odd <- seq(from = 1, to = nrow(iris), by = 2)
even <- odd + 1
X.train <- iris[odd,-5]
Class.train <- iris[odd,5]
X.test <- iris[even,-5]
Class.test <- iris[even,5]

# common EEE covariance structure (which is essentially equivalent to linear discriminant analysis)
irisMclustDA <- MclustDA(X.train, Class.train, modelType = "EDDA", modelNames = "EEE")
summary(irisMclustDA, parameters = TRUE)
summary(irisMclustDA, newdata = X.test, newclass = Class.test)

# common covariance structure selected by BIC
irisMclustDA <- MclustDA(X.train, Class.train, modelType = "EDDA")
summary(irisMclustDA, parameters = TRUE)
summary(irisMclustDA, newdata = X.test, newclass = Class.test)

# general covariance structure selected by BIC
irisMclustDA <- MclustDA(X.train, Class.train)
summary(irisMclustDA, parameters = TRUE)
summary(irisMclustDA, newdata = X.test, newclass = Class.test)

plot(irisMclustDA)
plot(irisMclustDA, dimens = 3:4)
plot(irisMclustDA, dimens = 4)

plot(irisMclustDA, what = "classification")
plot(irisMclustDA, what = "classification", newdata = X.test)
plot(irisMclustDA, what = "classification", dimens = 3:4)
plot(irisMclustDA, what = "classification", newdata = X.test, dimens = 3:4)
plot(irisMclustDA, what = "classification", dimens = 4)
plot(irisMclustDA, what = "classification", dimens = 4, newdata = X.test)

plot(irisMclustDA, what = "train&test", newdata = X.test)
plot(irisMclustDA, what = "train&test", newdata = X.test, dimens = 3:4)
plot(irisMclustDA, what = "train&test", newdata = X.test, dimens = 4)

plot(irisMclustDA, what = "error")
plot(irisMclustDA, what = "error", dimens = 3:4)
plot(irisMclustDA, what = "error", dimens = 4)
plot(irisMclustDA, what = "error", newdata = X.test, newclass = Class.test)
plot(irisMclustDA, what = "error", newdata = X.test, newclass = Class.test, dimens = 3:4)
plot(irisMclustDA, what = "error", newdata = X.test, newclass = Class.test, dimens = 4)

# simulated 1D data
n <- 250 
set.seed(1)
triModal <- c(rnorm(n,-5), rnorm(n,0), rnorm(n,5))
triClass <- c(rep(1,n), rep(2,n), rep(3,n))
odd <- seq(from = 1, to = length(triModal), by = 2)
even <- odd + 1
triMclustDA <- MclustDA(triModal[odd], triClass[odd])
summary(triMclustDA, parameters = TRUE)
summary(triMclustDA, newdata = triModal[even], newclass = triClass[even])
plot(triMclustDA)
plot(triMclustDA, what = "classification")
plot(triMclustDA, what = "classification", newdata = triModal[even])
plot(triMclustDA, what = "train&test", newdata = triModal[even])
plot(triMclustDA, what = "error")
plot(triMclustDA, what = "error", newdata = triModal[even], newclass = triClass[even])

# simulated 2D cross data
data(cross)
odd <- seq(from = 1, to = nrow(cross), by = 2)
even <- odd + 1
crossMclustDA <- MclustDA(cross[odd,-1], cross[odd,1])
summary(crossMclustDA, parameters = TRUE)
summary(crossMclustDA, newdata = cross[even,-1], newclass = cross[even,1])
plot(crossMclustDA)
plot(crossMclustDA, what = "classification")
plot(crossMclustDA, what = "classification", newdata = cross[even,-1])
plot(crossMclustDA, what = "train&test", newdata = cross[even,-1])
plot(crossMclustDA, what = "error")
plot(crossMclustDA, what = "error", newdata =cross[even,-1], newclass = cross[even,1])
# }