YplantQMC (version 0.6-6)

plot.plant3d: Plots a plant in 3D

Description

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.

Usage

"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), ...)
"plot"(x, whichrows = NA, png = FALSE, pngsuff = "", keepopen = !png, windowrect = c(50, 50, 800, 800), squarewidth = 25, skipexisting = FALSE, addfilename = FALSE, ...)
"plot"(x, ...)

Arguments

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.

Details

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).

See Also

crownhull

Examples

## 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)