coordProj {mclust} | R Documentation |
Plots coordinate projections given data in more than two dimensions and parameters of an MVN mixture model for the data.
coordProj(data, ..., dimens = c(1, 2), type = c("classification","uncertainty","errors"), ask = TRUE, quantiles = c(0.75, 0.95), symbols, scale = FALSE, identify = FALSE, CEX = 1, PCH = ".", xlim, ylim)
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.
|
... |
One or more of the following:
|
type |
Any subset of
c("classification","uncertainty","errors") . The function will
produce the corresponding plot if it has been supplied sufficient
information to do so. If more than one plot is possible then users
will be asked to choose from a menu if ask=TRUE .
|
ask |
A logical variable indicating whether or not a menu should be
produced when more than one plot is possible. The default is
ask=TRUE .
|
quantiles |
A vector of length 2 giving quantiles used in plotting uncertainty. The smallest symbols correspond to the smallest quantile (lowest uncertainty), medium-sized (open) symbols to points falling between the given quantiles, and large (filled) symbols to those in the largest quantile (highest uncertainty). The default is (0.75,0.95). |
symbols |
Either an integer or character vector assigning a plotting symbol to
each unique class in classification . Elements in
symbols correspond to classes in classification in
sorted order. Default: If G is the number of groups in the
classification, the first G symbols in
.Mclust\$symbols , otherwise if G is less than 27 then
the first G capital letters in the Roman alphabet.
|
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
|
identify |
A logical variable indicating whether or not to add a title to the plot identifying the dimensions used. |
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 classificatiion has not been specified for the data. The default value is a small dot ".". |
xlim, ylim |
Arguments specifying bounds for the ordinate, abscissa of the plot. This may be useful for when comparing plots. |
Coordinate projections of the data, possibly showing location of the mixture components, classification, uncertainty, and/or classification errors.
C. Fraley and A. E. Raftery (2002). Model-based clustering, discriminant analysis, and density estimation. Journal of the American Statistical Association 97:611-631. See http://www.stat.washington.edu/mclust.
C. Fraley and A. E. Raftery (2002). MCLUST:Software for model-based clustering, density estimation and discriminant analysis. Technical Report, Department of Statistics, University of Washington. See http://www.stat.washington.edu/mclust.
clPairs
,
randProj
,
mclust2Dplot
,
mclustOptions
,
do.call
data(iris) irisMatrix <- as.matrix(iris[,1:4]) irisClass <- iris[,5] msEst <- mstepVVV(irisMatrix, unmap(irisClass)) par(pty = "s", mfrow = c(1,2)) coordProj(irisMatrix,dimens=c(2,3), truth = irisClass, mu = msEst$mu, sigma = msEst$sigma, z = msEst$z) do.call("coordProj", c(list(data=irisMatrix, dimens=c(2,3), truth=irisClass), msEst))