tcsplot: Interactive Plot of a Tetrahedral Colorspace

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/tcsplot.R

Description

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

Plots points in a tetrahedral color space

Produces a 3D convex hull in tetrahedral color space

Usage

1
2
3
4
5
6
7
8
9
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, grid = TRUE, fill = TRUE)

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

tcsvol(tcsdata, col = "black", alpha = 0.2, grid.alpha = 1, grid = T,
  fill = T, lwd = 1)

Arguments

tcsdata

(required) a data frame, possibly a result from the colspace 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

color of the points in the plot (defaults to black)

vertexsize

size of the points at the vertices

achro

plot a point at the origin? (defaults to TRUE)

achrosize

size of the point in the achromatic center

achrocol

color of the point in the achromatic center

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)

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).

grid.alpha

transparecny of the volume polygon grid lines

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). tcsvol creates polygon based on points, determining the volume occupied by them in the colorspace. tcspoints adds points to the plot. Points are currently plotted only as spheres to maintain export capabilities.

tcspoints creates 3D points in a tetrahedral color space plot produced by tcsplot using functions of the package rgl, based on openGL capabilities.

tcsvol creates a 3D convex hull within a tcsplot object.

Author(s)

Rafael Maia rm72@zips.uakron.edu

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.

See Also

spheres3d,rgl.postscript, rgl.snapshot,rgl.material

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
## Not run: 
# For plotting
data(sicalis)
vis.sicalis <- vismodel(sicalis, visual = 'avg.uv')
tcs.sicalis <- colspace(vis.sicalis, space = 'tcs')
plot(tcs.sicalis, size = 0.005)
rgl.postscript('testplot.pdf',fmt='pdf') 
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') 
plot(tcs.crown, col ='blue')
points(tcs.breast, col ='red')

# For plotting convex hull
plot(tcs.sicalis, col = 'blue', size = 0.005)
vol(tcs.sicalis)

## End(Not run)

pavo documentation built on May 30, 2017, 12:42 a.m.

Search within the pavo package
Search all R packages, documentation and source code