deformGrid3d: visualise differences between two superimposed sets of 3D...

In Morpho: Calculations and Visualisations Related to Geometric Morphometrics

visualise differences between two superimposed sets of 3D landmarks

Description

visualise differences between two superimposed sets of 3D landmarks by deforming a cubic grid based on a thin-plate spline interpolation

Usage

deformGrid3d(
  matrix,
  tarmatrix,
  ngrid = 0,
  align = FALSE,
  lwd = 1,
  showaxis = c(1, 2),
  show = c(1, 2),
  lines = TRUE,
  lcol = 1,
  add = FALSE,
  col1 = 2,
  col2 = 3,
  type = c("s", "p"),
  size = NULL,
  pcaxis = FALSE,
  ask = TRUE,
  margin = 0.2,
  createMesh = FALSE,
  slice1 = NULL,
  slice2 = NULL,
  slice3 = NULL,
  gridcol = 1,
  gridwidth = 1,
  ...
)

Arguments

matrix	reference matrix containing 3D landmark coordinates or mesh of class "mesh3d"
tarmatrix	target matrix containing 3D landmark coordinates or mesh of class "mesh3d"
ngrid	number of grid lines to be plotted; ngrid=0 suppresses grid creation.
align	logical: if TRUE, tarmatrix will be aligned rigidly to matrix
lwd	width of lines connecting landmarks.
showaxis	integer (vector): which dimensions of the grid to be plotted. Options are combinations of 1,2 and 3.
show	integer (vector): if c(1:2) both configs will be plotted, show = 1 only plots the reference and show = 2 the target
lines	logical: if TRUE, lines between landmarks will be plotted.
lcol	color of lines
add	logical: add to existing rgl window.
col1	color of "matrix"
col2	color of "tarmat"
type	"s" renders landmarks as spheres; "p" as points - much faster for very large pointclouds.
size	control size/radius of points/spheres
pcaxis	logical: align grid by shape's principal axes.
ask	logical: if TRUE for > 1000 coordinates the user will be asked to prefer points over spheres.
margin	margin around the bounding box to draw the grid
createMesh	logical: if TRUE, a triangular mesh of spheres and displacement vectors (can take some time depending on number of reference points and grid density).
slice1	integer or vector of integers: select slice(s) for the dimensions
slice2	integer or vector of integers: select slice(s) for the dimensions
slice3	integer or vector of integers: select slice(s) for the dimensions
gridcol	define color of grid
gridwidth	integer: define linewidth of grid
...	additional parameters passed to rotonto in case align=TRUE

Value

if createMesh=TRUE, a mesh containing spheres of reference and target as well as the displacement vectors is returned. Otherwise the knots of the displaced grid is returned.

Author(s)

Stefan Schlager

See Also

tps3d

Examples

if (interactive()){
data(nose)
deformGrid3d(shortnose.lm,longnose.lm,ngrid=10)

## select some slices
deformGrid3d(shortnose.lm,longnose.lm,showaxis=1:3,ngrid=10,slice1=2,slice2=5,slice3=7)
}

Morpho documentation built on Feb. 16, 2023, 10:51 p.m.