plotspec: Plot 3D specimen, fixed landmarks and surface semilandmarks

Description

A function to plot three-dimensional (3D) specimen along with its landmarks.

Usage

plotspec(
  spec,
  digitspec,
  fixed = NULL,
  fixed.pt.col = "red",
  fixed.pt.size = 10,
  mesh.ptsize = 1,
  centered = FALSE,
  ...
)

Arguments

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.

Author

Erik Otarola-Castillo, Emma Sherratt, Antigoni Kaliontzopoulou, & Michael Collyer

Details

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.

Examples

Run this code

if (FALSE) {

 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)
 }