Plot the output from morphogrid(), for 3-dimensional
morphometric (landmark) data. Used internally.
plot_morphogrid3d(
x = NULL,
y = NULL,
morphogrid,
refshape,
template = NULL,
links = NULL,
ordtype,
axes,
rotmat = NULL,
xlim = NULL,
ylim = NULL,
xlab = NULL,
ylab = NULL,
adj_frame = c(1, 1),
cex.ldm,
col.ldm,
col.models,
lwd.models,
size.models,
alpha.models = 1,
bg.models,
asp.models,
plot = TRUE,
models = TRUE
)Optional vector with a non-morphometric variable to be plotted in the x axis.
Optional vector with a non-morphometric variable to be plotted in the y axis.
An object containing the output of morphogrid.
reference shape (i.e., the mean landmark configuration)
corresponding to the mesh provided in template.
An optional "mesh3d" object containing
geometry of the structure the landmarks were placed on (for 3D shape data),
corresponding to the mean shape of the sample, which will be warped using
TPS interpolation to produce the set of background shell models.
A list with the indices of the coordinates defining the
wireframe (following the format used in Morpho).
Character; method used for multivariate ordination
("prcomp", "bg_prcomp", "phy_prcomp",
"pls_shapes" or "phy_pls_shapes").
Numeric of length 2, indicating the axes to be plotted.
Optional rotation matrix for background shape models. If
NULL, the user will be asked to define a preferred orientation.
Standard arguments passed to the generic plot function.
Numeric of length 2, providing a posteriori scaling factors for the width and height of the frame, respectively.
Numeric; size of landmarks/semilandmarks in the background models.
The color of landmarks/semilandmarks in the background models.
The color for wireframes/outlines.
Numeric; the width of the lines in wireframes/outlines.
Numeric; size factor for shape models.
Numeric; transparency factor for background models.
Background color for meshes.
Numeric; the y/x aspect ratio of shape models.
Logical; whether to plot morphospace.
Logical; whether to plot background shape models.
This function allows the user to choose the orientation of the 3D
models by interactively rotating a shape model. Do not close the rgl
window, or minimize it actively (just bring back Rstudio to the front and
let the device get minimized pasively). The process of morphospace
generation is rather slow, specially if a mesh is provided for
template, a large number of shape models is asked, and/or
alpha.models value is lower than 1.
#load data and packages
library(geomorph)
data("shells3D")
shapes <- shells3D$shapes
#perform pca on tails shapes
pca <- prcomp(two.d.array(shapes))
#generate grid of shape models sampling the range of variation
#at 4 locations (the 4 corners of the scatterplot)
shapes_grid <- morphogrid(ordination = pca, axes = c(1,2), datype = "landm",
k = ncol(shapes), p = nrow(shapes),
nh = 2, nv = 2)
#get meanshape
meanshape <- expected_shapes(shapes)
if (FALSE) {
#plot grid (shape coordinates only)
plot_morphogrid3d(morphogrid = shapes_grid, refshape = meanshape,
ordtype = "prcomp", axes = c(1,2), col.ldm = 1,
cex.ldm = 1, col.models = 1, lwd.models = 1,
bg.models = "gray", size.models = 2, asp.models = 1)
#get shape corresponding to shells3D$mesh_meanspec using
#geomorph::findMeanSpec, then get mesh corresponding to mean shape using
#Morpho::tps3d
meanspec_id<- findMeanSpec(shapes)
meanspec_shape <- shapes[,,meanspec_id]
meanmesh <- tps3d(x = shells3D$mesh_meanspec , refmat = meanspec_shape,
tarmat = meanshape)
#plot grid (includinh mesh template)
plot_morphogrid3d(morphogrid = shapes_grid, template = meanmesh,
refshape = meanshape, ordtype = "prcomp", axes = c(1,2),
col.ldm = 1, cex.ldm = 1, col.models = 1, lwd.models = 1,
bg.models = "gray", size.models = 2, asp.models = 1)
}