plotspec | R Documentation |
A function to plot three-dimensional (3D) specimen along with its landmarks.
plotspec(
spec,
digitspec,
fixed = NULL,
fixed.pt.col = "red",
fixed.pt.size = 10,
mesh.ptsize = 1,
centered = FALSE,
...
)
spec |
An object of class shape3d/mesh3d, or matrix of 3D vertex coordinates. |
digitspec |
Name of data matrix containing 3D fixed and/or surface sliding coordinates. |
fixed |
Numeric The number of fixed template landmarks (listed first in digitspec) |
fixed.pt.col |
The color for plotting fixed template landmarks (if any) |
fixed.pt.size |
The size for plotting fixed template landmarks (if any) |
mesh.ptsize |
Numeric Size to plot the mesh points (vertices), e.g. 0.1 for dense meshes, 3 for sparse meshes |
centered |
Logical Whether the data matrix is in the surface mesh coordinate system (centered = "FALSE") or if the data were collected after the mesh was centered (centered = "TRUE")- see details. |
... |
additional parameters which will be passed to rgl-plot3d or rgl-points3d. |
Function to plot 3D specimens along with their digitized "fixed" landmarks and semilandmarks
"surface sliders" and "curve sliders". If specimen is a 3D surface (class shape3d/mesh3d) mesh is plotted.
For visualization purposes, 3D coordinate data collected using digit.fixed
or
digitsurface
and buildtemplate
prior to build 1.1-6 were centered by default.
Therefore use this function with centered = "TRUE". Data collected outside geomorph should be read using
centered = "FALSE". The function assumes the fixed landmarks are listed at the beginning of
the coordinate matrix (digitspec).
This function is a wrapper for several functions in the rgl
package.
Although there is some allowance for arguments to be passed to rgl
functions,
some override of rgl-plot3d arguments is required. Errors that result from trying
to pass rgl-plot3d or rgl-points3d arguments should inspire the user
to find solutions with rgl
core functions.
Erik Otarola-Castillo, Emma Sherratt, Antigoni Kaliontzopoulou, & Michael Collyer
warpRefMesh
read.ply
rgl
(used in 3D plotting)
## Not run:
data(scallopPLY)
ply <- scallopPLY$ply
digitdat <- scallopPLY$coords
plotspec(spec = ply, digitspec = digitdat, fixed = 16,
centered = TRUE, fixed.pt.col = "red",
fixed.pt.size = 15, col = "blue", size = 5)
## End(Not run)
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