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

In EmSherratt/geomorph: Geometric Morphometric Analyses of 2D/3D Landmark Data

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.

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 package. Although there is some allowance for arguments to be passed to rgl-package 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-package core functions.

Author(s)

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

See Also

warpRefMesh

read.ply

rgl-package (used in 3D plotting)

Examples

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)

EmSherratt/geomorph documentation built on June 24, 2022, 11:05 p.m.