vegan3d-package: Dynamic and Static 3D and Interactive 2D Plots for Ordination

In vegan3d: Static and Dynamic 3D and Editable Interactive Plots for the 'vegan' Package

Dynamic and Static 3D and Interactive 2D Plots for Ordination

Description

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.

Index: This package was not yet installed at build time.

Drawing with rgl Functions

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.

Drawing with scatterplot3d and lattice 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.

Editable Graphics with Tcl/Tk based orditkplot

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.

vegan3d documentation built on Aug. 26, 2025, 5:07 p.m.