Plot shape differences between a reference and target specimen
Function plots shape differences between a reference and target specimen
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,
...
)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 |
useRefPts |
An option (logical value) to use reference configuration points rather than target configuration points (when method = "TPS") |
... |
Additional parameters not covered by |
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).
If using method="surface", function will return the warped mesh3d object.
Dean Adams, Emma Sherratt, Antigoni Kaliontzopoulou & Michael Collyer
Claude, J. 2008. Morphometrics with R. Springer, New York.
rgl-package (used in 3D plotting)
# 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)
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