plotRefToTarget: Plot shape differences between a reference and target...
In geomorph: Geometric Morphometric Analyses of 2D and 3D Landmark Data

plotRefToTarget

R Documentation

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,
  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.

Additionally, if a matrix of links is provided, the landmarks 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.

Four distinct methods for plots are available:

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.
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 overlaying those of the reference.
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, Antigoni Kaliontzopoulou & Michael Collyer

References

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

Examples

## Not run: 

# 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], method = "vector", 
 outline = plethodon$outline, mag = 2.5)
 plotRefToTarget(ref, Y.gpa$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)

## End(Not run)

geomorph documentation built on June 24, 2024, 5:07 p.m.