Hulls: Groups' hulls

Description

Groups' hulls with centroids calculation

Usage

Hulls(pts, groups, match.color=TRUE, usecolors=NULL, plot=TRUE, centers=FALSE,
 c.pch=0, c.cex=3, outliers=TRUE, coef=1.5, ...)

Arguments

pts

Data points to plot

groups

Grouping variable, any type

match.color

Match color

usecolors

Which colors to use (similar to plot(..., col=))

plot

Plot?

centers

Show centers?

c.pch

Color of center points

c.cex

Scale of center points

outliers

Include outliers?

coef

Determines how to detect outliers, see 'coef' from 'boxplot.stats()'

...

Arguments to 'lines()'

Value

Invisibly outputs list of hulls with coordinates, and possibly also with 'centers' and 'outliers' components

Details

Groups' hulls with optional centroids calculation (requires 'PBSmapping').

If 'outliers=FALSE', uses 'boxplot.stats()' to detect outliers (points which are most distant from centers). This option automatically switch 'centers=TRUE' so if you want to plot smoothed hulls but do not want to plot centers, use something like 'c.pch=""' or 'c.cex=0'. This could be used for cluster sharpening.

Examples

Run this code

# NOT RUN {
iris.p <- prcomp(iris[, -5], scale=TRUE)$x[, 1:2]
plot(iris.p, type="n", xlab="PC1", ylab="PC2")
pal <- rainbow(3)
text(iris.p, labels=abbreviate(iris[, 5], 1, method="both.sides"),
 col=pal[as.numeric(iris[, 5])])
Hulls(iris.p, iris[, 5], centers=TRUE, usecolors=pal)

## smoothed hulls
iris.p <- prcomp(iris[, 1:4], scale=TRUE)$x[, 1:2]
plot(iris.p, col=iris$Species, xlab="PC1", ylab="PC2")
ppts <- Hulls(iris.p, iris[, 5], centers=TRUE, outliers=FALSE, coef=2)
ppts$outliers
# }