Interactive plot of a tetrahedral colourspace

Produces an interactive 3D plot of a tetrahedral colourspace using OpenGL capabilities.

Plots points in a tetrahedral colour space

tcsplot(
  tcsdata,
  size = 0.02,
  alpha = 1,
  col = "black",
  vertexsize = 0.02,
  achro = TRUE,
  achrosize = 0.01,
  achrocol = "grey",
  lwd = 1,
  lcol = "lightgrey",
  new = FALSE,
  hspin = FALSE,
  vspin = FALSE,
  floor = TRUE,
  gamut = FALSE
)

tcspoints(tcsdata, size = 0.02, col = "black", alpha = 1)

tcsvol(
  tcsdata,
  type = c("convex", "alpha"),
  avalue = "auto",
  col = "black",
  alpha = 0.2,
  grid.alpha = 1,
  grid = TRUE,
  fill = TRUE,
  lwd = 1
)

Arguments

tcsdata: (required) a data frame, possibly a result from the colspace() or tcspace() function, containing values for the 'x', 'y' and 'z' coordinates as columns (labeled as such).
size: size of the points in the plot (defaults to 0.02)
alpha: transparency of points (or volume fill in tcsvol())
col: colour of the points in the plot (defaults to black)
vertexsize: size of the points at the vertices
achro: should a point be plotted at the origin (defaults to TRUE)?
achrosize: size of the point at the origin when achro = TRUE (defaults to 0.8).
achrocol: color of the point at the origin achro = TRUE (defaults to 'grey').
lwd, lcol: graphical parameters for the edges of the tetrahedron.
new: should a new 3D plot be called (defaults to FALSE)?
hspin: if TRUE, the graphic will spin horizontally (around the 'z' axis)(defaults to FALSE)
vspin: if TRUE, the graphic will spin vertically (around the 'x' axis)(defaults to FALSE)
floor: if TRUE, a reference xy plane is plotted under the tetrahedron (defaults to TRUE)
gamut: logical. Should the polygon showing the possible colours given visual system and illuminant used in the analysis (defaults to FALSE). This option currently only works when qcatch = Qi.
type: accepts a vector of length 1 or 2 with 'p' for points and/or 'l' for lines from the point to the base of the tetrahedron.
avalue: if type = "alpha", which alpha parameter value should be used to compute the alphashape. avalue = "auto" (default) finds and use the \(\alpha^*\) value as defined in Gruson (2020).
grid.alpha: transparency of the volume polygon grid lines
grid: if TRUE, connects the polygon outlining the volume occupied by points (defaults to TRUE)
fill: if TRUE, fills the volume occupied by points (WARNING: transparency is not saved properly if exported using rgl.postscript)(defaults to TRUE).

Value

tcsplot() creates a 3D plot using functions of the package rgl, based on openGL capabilities. Plot is interactive and can be manipulated with the mouse (left button: rotate along 'z' axis; right button: rotate along 'x' axis; third button: zoom).

tcspoints() adds points to the plot. Points are currently plotted only as spheres to maintain export capabilities.

tcsvol() creates a 3D colour volume within a tcsplot object.

References

Stoddard, M. C., & Prum, R. O. (2008). Evolution of avian plumage color in a tetrahedral color space: A phylogenetic analysis of new world buntings. The American Naturalist, 171(6), 755-776.

Endler, J. A., & Mielke, P. (2005). Comparing entire colour patterns as birds see them. Biological Journal Of The Linnean Society, 86(4), 405-431.

Author

Rafael Maia rm72@zips.uakron.edu

Examples

# For plotting
data(sicalis)
vis.sicalis <- vismodel(sicalis, visual = "avg.uv")
tcs.sicalis <- colspace(vis.sicalis, space = "tcs")
tcsplot(tcs.sicalis, size = 0.005)
rgl::rgl.postscript("testplot.pdf", fmt = "pdf")
#> Warning: Postscript conversion failed
rgl::rgl.snapshot("testplot.png")

# For adding points
patch <- rep(c("C", "T", "B"), 7)
tcs.crown <- subset(tcs.sicalis, "C")
tcs.breast <- subset(tcs.sicalis, "B")
tcsplot(tcs.crown, col = "blue")
tcspoints(tcs.breast, col = "red")


# For plotting convex hull
tcsplot(tcs.sicalis, col = "blue", size = 0.005)
tcsvol(tcs.sicalis)