cluster.plot: Plot data clusters

In shapeR: Collection and Analysis of Otolith Shape Data

Plot data clusters

Description

Plots data clusters

Usage

cluster.plot( ddata, classes, main="", col.stock=NULL,
              plotCI = FALSE, conf.level = 0.68, ...)

Arguments

ddata	Matrix of points
classes	A factor including the cluster values
main	Title for the plot
col.stock	Colors for the plotted classes
plotCI	Plot means with confidence intervals
conf.level	The confidence interval for the standard error of the mean
...	Additional parameters to be passed to 'plot' or 'ldahist' if one dimension

Value

None

Author(s)

Lisa Anne Libungan

References

Oksanen, J., Blanchet, F.G., Kindt, R., Legendre, P., Minchin, P.R., O'Hara, R.B., Simpson, G.L., Solymos, P., Stevens, M.H.H. and Wagner, H. (2013). vegan: Community Ecology Package. R package version 2.0-10.

Examples

data(shape)
library(vegan)
cap.res = capscale(getStdWavelet(shape) ~ getMasterlist(shape)$pop)

eig=eigenvals(cap.res,constrained=TRUE)
eig.ratio = eig/sum(eig)

cluster.plot(scores(cap.res)$sites[,1:2],getMasterlist(shape)$pop
,plotCI=TRUE
,xlab=paste("CAP1 (",round(eig.ratio[1]*100,1),"%)",sep="")
,ylab=paste("CAP2 (",round(eig.ratio[2]*100,1),"%)",sep="")
,main="Canonical clustering"
)

shapeR documentation built on Nov. 22, 2022, 1:07 a.m.