geomorph (version 1.1-1)

plotAllSpecimens: Plot landmark coordinates for all specimens

Description

Function plots landmark coordinates for a set of specimens

Usage

plotAllSpecimens(A, mean = TRUE, links = NULL,
    pointscale = 1, meansize = 2)

Arguments

A

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

mean

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

links

An optional matrix defining for links between landmarks

pointscale

An optional value defining the size of the points for all specimens

meansize

An optional value defining the size of the points representing the average specimen

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.

Examples

# Example 1: Two-dimensional landmark data
data(plethodon)
Y.gpa<-gpagen(plethodon$land)    #GPA-alignment

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

# Example 2: Three-dimensional landmark data
data(scallops)
Y.gpa<-gpagen(A=scallops$coorddata, curves=scallops$curvslide, surfaces=scallops$surfslide)

plotAllSpecimens(Y.gpa$coords)