geomorph (version 2.1.2)

plotRefToTarget: Plot shape differences between a reference and target specimen

Description

Function plots shape differences between a reference and target specimen

Usage

plotRefToTarget(M1, M2, mesh = NULL, outline = NULL, method = c("TPS",
  "vector", "points", "surface"), mag = 1, links = NULL, ...)

Arguments

M1

Matrix of landmark coordinates for the first (reference) specimen

M2

Matrix of landmark coordinates for the second (target) specimen

mesh

A mesh3d object for use with {method="surface"}

outline

An x,y curve or curves warped to the reference (2D only)

method

Method used to visualize shape difference; see below for details

mag

The desired magnification to be used when visualizing the shape difference (e.g., mag=2)

links

An optional matrix defining for links between landmarks

...

Parameters to be passed to plot, plot3d or shade3d

Value

• If using {method="surface"}, function will return the warped mesh3d object.

Details

The function generates a plot of the shape differences of a target specimen relative to a reference specimen. The option {mag} allows the user to indicates the degree of magnification to be used when displaying the shape difference. The function will plot either two- or three-dimensional data. For two-dimensional data and thin-plate spline deformation plots, the user may also supply boundary curves of the object, which will be deformed from the reference to the target specimen using the thin-plate spline. Such curves are often useful in describing the biological shape differences expressed in the landmark coordinates. Note that to utilize this option, a boundary curve from a representative specimen must first be warped to the reference specimen using warpRefOutline. Four distinct methods for plots are available:

1. TPS

a thin-plate spline deformation grid is generated. For 3D data, this method will generate thin-plate spline deformations in the x-y and x-z planes. A boundary curve will also be deformed if provided by the user. vector: a plot showing the vector displacements between corresponding landmarks in the reference and target specimen is shown. points a plot is displayed with the landmarks in the target (black) overlaying those of the reference (gray). 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. surface a mesh3d surface is warped using thin-plate spline (for 3D data only). Requires mesh3d object in option {mesh}, made using warpRefMesh.

References

Claude, J. 2008. Morphometrics with R. Springer, New York.

Examples

data(plethodon)
Y.gpa<-gpagen(plethodon$land)    #GPA-alignment
ref<-mshape(Y.gpa$coords)
plotRefToTarget(ref,Y.gpa$coords[,,39])
plotRefToTarget(ref,Y.gpa$coords[,,39],mag=2,outline=plethodon$outline)   #magnify difference by 2X
plotRefToTarget(ref,Y.gpa$coords[,,39],method="vector",mag=3)
plotRefToTarget(ref,Y.gpa$coords[,,39],method="points",outline=plethodon$outline)


# Three dimensional data

data(scallops)
Y.gpa<-gpagen(A=scallops$coorddata, curves=scallops$curvslide, surfaces=scallops$surfslide)
ref<-mshape(Y.gpa$coords)
plotRefToTarget(ref,Y.gpa$coords[,,1],method="points")