The vegan3d package provides 3D plotting for all vegan
ordination methods or any other ordination method that vegan
scores function can handle. It can also display
hclust results in 3D over a 2D plane. Dynamic 3D plots
are based on the rgl package and static plots are drawn with
scatterplot3d and lattice packages. The package
also provides 2D editable interactive plots for ordination. The points
are fixed at their ordination scores, but labels can be moved to
better position, and the result can be saved in various graphics
formats or saved in R session and re-created with R plot
commands.
tools:::Rd_package_indices("vegan3d")
The rgl graphics are dynamic 3D plots that can be spinned and
zoomed with mouse. The vegan3d package provides interface to
ordination and clustering objects. The functions use rgl setting
and conventions and do not change the user settings. For general
configuration of the plots, users should check rgl
documentation. For instance, general look and feel of drawn items can
be configured with material3d.
The rgl package may not be available on all platforms, and
the package is not automatically loaded. If you want to use
rgl functions, you must either prefix commands with
rgl:: or call library(rgl) in your session. If you
cannot launch rgl window (or widget) on your platform, check
the instructions on the rgl. In most cases, it should be
possible to use rgl at least on a compatible browser.
Function ordirgl is similar to
ordiplot in vegan, and any ordination
result can be drawn with similar conventions. Functions with
orgl prefix add items to existing plots, for instance,
orglellipse is analogous to
ordiellipse.
Function ordirgltree draws an hclust
dendrogram over a plane. It was originally developed for 2D ordination
planes, but any other plane can be used, for instance a projected map.
Functions rgl.isomap and rgl.renyiaccum
provide alternative dynamic 3D plots for vegan
isomap and renyiaccum
functions.
The scatterplot3d package draws static 3D graphics, and
vegan3d provides an interface for ordination and clustering
objects. You must consult the
scatterplot3d documentation for
configuring your plots. vegan3d function
ordilattice3d is similar, but is based on the
lattice package, and can be modified using lattice
commands and arguments.
Function ordiplot3d is similar to ordirgl
or ordiplot and draws a static 3D plot in the
standard graphical device. It returns invisibly a plotting object
which contains the projected points, and vegan ordi*
prefix functions can use this object. For instance,
ordiellipse will add ellipses on the projected
points.
Function ordilattice3d is a similar to
ordiplot3d in lattice graphics, but currently more
limited than ordiplot3d. The lattice package is not
loaded and you need to use library(lattice) or prefix your
lattice commands with lattice::. There are obvious ways
of improving the function. Contributions are welcome.
Function orditree3d will draw an hclust
dendrogram over a plane similarly as ordirgltree.
Function draws ordination scores in a new Tcl/Tk window with fixed points and their editable labels. The labels can be moved to better positions which helps with crowded plots. It is also possible to zoom into graph to display only a part of the complete graph. The edited result can be saved in various graphical formats or saved as an R object in the session for further manipulation or re-creating the graph with standard R plotting tools.
Tcl/Tk is not available on all platforms or R installations. Use
command capabilities("tcltk") to see if you have it in your
system.
There are obvious ways of improving the function. Contributions are welcome.