Plot shape differences between a reference and target specimen

Description

Function plots shape differences between a reference and target specimen

Usage

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

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

label

A logical value indicating whether landmark numbers will be plotted

axes

A logical value indicating whether the box and axes should be plotted (points and vector only)

gridPars

An optional object made by gridPar

useRefPts

An option (logical value) to use reference configuration points rather than target configuration points (when method = "TPS")

...

Additional parameters not covered by gridPar to be passed to plot, plot3d or shade3d

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

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# 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)

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