plot.plant3d: Plots a plant in 3D
In YplantQMC: Plant Architectural Analysis with Yplant and QuasiMC

Description Usage Arguments Details Author(s) See Also Examples

Based on a plant constructed with constructplant, plots the plant in 3D using the rgl package. Optionally adds the convex hull to the plot.

See the function crownhull for details of the convex hull algorithm.

## S3 method for class 'plant3d'
plot(x, noleaves = FALSE, squarewidth = 250,
  addcrownhull = FALSE, hullalpha = 0.4, leaffill = TRUE,
  leafoutline = TRUE, stems = TRUE, cylinderstems = stems,
  leafcolor = "forestgreen", markleaves = NULL, markcolor = "red",
  stemcol = "black", branchcol = "black", petiolecol = "brown",
  add = FALSE, shiftxyz = c(0, 0, 0), ...)

## S3 method for class 'plant3dlist'
plot(x, whichrows = NA, png = FALSE, pngsuff = "",
  keepopen = !png, windowrect = c(50, 50, 800, 800), squarewidth = 25,
  skipexisting = FALSE, addfilename = FALSE, ...)

## S3 method for class 'stand3d'
plot(x, ...)

`x`	Object of class `plant3d` or `plant3dlist`.
`noleaves`	Logical. If TRUE, leaves are not plotted.
`squarewidth`	Width of the square to be plotted at the ground surface.
`addcrownhull`	Logical. If TRUE, a convex hull is added to the plot.
`hullalpha`	Opacity of the convex hull.
`leaffill`	Logical. If TRUE, the default, fills in the leaves.
`leafoutline`	Logical. If TRUE, plots leaf outlines.
`stems`	Logical. If TRUE, plots the stems (black) and branches .
`cylinderstems`	Logical. If TRUE, plots the stems as cylinder sections given the diameter in the plant file.
`leafcolor`	Color of the filled leaves. Can only specify one color.
`markleaves, markcolor`	A vector of leaf numbers to 'mark', using 'markcolor'.
`stemcol, branchcol, petiolecol`	Color of the stems, branches, petioles
`add`	Logical. If TRUE (defaults to FALSE), adds this plant to an existing scene.
`shiftxyz`	Vector of x,y,z coordinates to shift the plant (see Examples).
`whichrows`	Which of the plants in the `plant3dlist` object to plot. Defaults to all.
`png`	If TRUE, saves a PNG snapshot of every plant plotted.
`pngsuff`	A suffix to add to the filename (defaults to pfile.PNG).
`keepopen`	Whether to keep all windows open. Max number of windows is 10.
`windowrect`	Size of the `rgl` window (see `open3d`). Affects PNG quality.
`skipexisting`	If PNG=TRUE, whether to skip plants that are already saved to disk.
`addfilename`	If TRUE, places a label of the pfile on the plot (currently poorly placed).
`...`	Further arguments passed to `plot3d` in the `rgl` package.

Some of the hard work, figuring out the X,Y,Z coordinates of the leaf tip and leaf sides, is directly taken from the original Yplant Delphi code (in the non-visible function madeleafdirection).

Remko Duursma. Robert Pearcy for the Y-plant code.

crownhull

## Not run: 
# Construct a plant like this:
# myplant <- constructplant("somepfile.p","aleaf.l")

# Standard plot (using built-in sugar maple):
plot(sugarmaple)

# Add a convex hull.
plot(sugarmaple, addcrownhull=TRUE)

# Plot two plants in one scene (second plant is moved 750mm in the x-direction)
plot(sugarmaple)
plot(sugarmaple, shiftxyz=c(750,0,0), add=TRUE)

# Mark the first 10 leaves in red (i.e. first 10 leaves in P file):
plot(sugarmaple, markleaves=1:10)

# Mark all leaves on the plant that have a leaf angle > 45.
plot(toona, markleaves=which(toona$leafdata$ang > 45))

# Plot the stems (and branches) only:
plot(pilularis, noleaves=TRUE)

# Plot many plants.
# First organize a 'leafplantkey', a comma-separated file that links each pfile to an lfile.
# See the online manual for an example, or the help file for 'constructplant'.
myplants <- readplantlist(lpk="leafplantkey.txt")
plot(myplants, png=TRUE, addfilename=TRUE)


## End(Not run)