Plot landmark coordinates for all specimens
Function plots landmark coordinates for a set of specimens
plotAllSpecimens( A, mean = TRUE, links = NULL, label = FALSE, plot.param = list() )
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) |
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).
Dean Adams
rgl-package (used in 3D plotting)
data(plethodon) Y.gpa<-gpagen(plethodon$land) #GPA-alignment plotAllSpecimens(Y.gpa$coords,links=plethodon$links)
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