plotHotellingEllipse: Hotelling ellipse

In svkucheryavski/mdatools: Multivariate Data Analysis for Chemometrics

Hotelling ellipse

Description

Add Hotelling ellipse to a scatter plot

Usage

plotHotellingEllipse(p, conf.lim = 0.95, col = "#a0a0a0", lty = 3, ...)

Arguments

p	plot series (e.g. from PCA scores plot)
conf.lim	confidence limit
col	color of the ellipse line
lty	line type (e.g. 1 for solid, 2 for dashed, etc.)
...	any argument suitable for lines function

Details

The method is created to be used with PCA and PLS scores plots, so it shows the statistical limits computed using Hotelling T^2 distribution in form of ellipse. The function works similar to plotConvexHull and plotConfidenceEllipse but does not require grouping of data points. Can be used together with functions plotScores.pca, plotScores.ldecomp, plotXScores.pls, plotXScores.plsres.

See examples for more details.

Examples

# create PCA model for People data
data(people)
m <- pca(people, 4, scale = TRUE)

# make scores plot and show Hotelling ellipse with default settings
p <- plotScores(m, xlim = c(-8, 8), ylim = c(-8, 8))
plotHotellingEllipse(p)

# make scores plot and show Hotelling ellipse with manual settings
p <- plotScores(m, xlim = c(-8, 8), ylim = c(-8, 8))
plotHotellingEllipse(p, conf.lim = 0.99, col = "red")

# in case if you have both calibration and test set, 'plotScores()' returns
# plot series data for both, so you have to subset it and take the first series
# (calibration set) as shown below.
ind <- seq(1, 32, by = 4)
xc <- people[-ind, , drop = FALSE]
xt <- people[ind, , drop = FALSE]
m <- pca(xc, 4, scale = TRUE, x.test = xt)

p <- plotScores(m, xlim = c(-8, 8), ylim = c(-8, 8))
plotHotellingEllipse(p[[1]])

svkucheryavski/mdatools documentation built on Aug. 4, 2024, 2:24 p.m.