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: A 3D array (p x k x n) containing Procrustes shape variables 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 plot 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)

Author

Dean Adams

Details

The function creates a plot of the landmark coordinates for all specimens. This is useful for examining patterns of variation in Procrustes shape variables, after a GPA has been performed. 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

Run this code

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

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