geomorph (version 3.0.3)

plotAllSpecimens: Plot landmark coordinates for all specimens

Description

Function plots landmark coordinates for a set of specimens

Usage

plotAllSpecimens(A, mean = TRUE, links = NULL, label = FALSE,
  plot.param = list())

Arguments

A

An array (p x k x n) containing GPA-aligned coordinates for a set of specimens

mean

A logical value indicating whether the mean shape should be included in the plot

links

An optional matrix defining for links between landmarks (only if mean=TRUE)

label

A logical value indicating whether landmark numbers will be plotted (only if mean=TRUE)

plot.param

A list of plotting parameters for the points (pt.bg, pt.cex), mean (mean.bg, mean.cex), links (link.col, link.lwd, link.lty) and landmark labels (txt.cex, txt.adj, txt.pos, txt.col)

Details

The function creates a plot of the landmark coordinates for all specimens. This is useful for examining patterns of shape variation after GPA. If "mean=TRUE", the mean shape will be calculated and added to the plot. Additionally, if a matrix of links is provided, the landmarks of the mean shape will be connected by lines. The link matrix is an m x 2 matrix, where m is the desired number of links. Each row of the link matrix designates the two landmarks to be connected by that link. The function will plot either two- or three-dimensional data (e.g. see define.links).

Examples

data(plethodon) 
Y.gpa<-gpagen(plethodon$land)    #GPA-alignment

plotAllSpecimens(Y.gpa$coords,links=plethodon$links)