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, label = FALSE,
  gridPars = NULL, useRefPts = FALSE, ...)

Arguments

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.

2. vector: a plot showing the vector displacements between corresponding landmarks in the reference and target specimen is shown.

3. 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.

4. surface a mesh3d surface is warped using thin-plate spline (for 3D data only). Requires mesh3d object in option mesh, made using warpRefMesh.

This function combines numerous plotting functions found in Claude (2008).

Value

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

Author(s)

Dean Adams, Emma Sherratt & Michael Collyer

References

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

See Also

gridPar

define.links

warpRefMesh

warpRefOutline

Examples

# Two dimensional data
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$outline)   #magnify by 2X
plotRefToTarget(ref,Y.gpa$coords[,,39],method="vector",mag=3)
plotRefToTarget(ref,Y.gpa$coords[,,39],method="points",outline=plethodon$outline)
plotRefToTarget(ref,Y.gpa$coords[,,39],gridPars=gridPar(pt.bg = "green", pt.size = 1),
method="vector",mag=3)

# 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$coords[,,1],method="points")
# scallinks <- matrix(c(1,rep(2:16, each=2),1), nrow=16, byrow=TRUE)
# plotRefToTarget(ref,Y.gpa$coords[,,1],gridPars=gridPar(tar.pt.bg = "blue", tar.link.col="blue",
# tar.link.lwd=2), method="points", links = scallinks)

Results