View source: R/plotAllSpecimens.r
plotAllSpecimens | R Documentation |
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)
## Not run:
data(plethodon)
Y.gpa <- gpagen(plethodon$land) #GPA-alignment
plotAllSpecimens(Y.gpa$coords, links = plethodon$links)
## End(Not run)
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