vegan3d-package {vegan3d}

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 the scatterplot3d package. 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 of help topics:

ordiplot3d              Three-Dimensional Ordination Graphics
ordirgl                 Three-Dimensional Dynamic Ordination Graphics
orditkplot              Ordination Plot with Movable Labels
orditree3d              Draw Cluster Tree over a Plane
rgl.isomap              Dynamic 3D plot of isomap ordination.
rgl.renyiaccum          Dynamic Perspective Plot of Renyi Diversity
                        Accumulation
vegan3d-package         Dynamic and Static 3D and Interactive 2D Plots
                        for Ordination

Drawing with rgl Functions

The rgl graphics are dynamic 3D plots that can be spinned and zoomed by 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 in all platforms, and therefore the package is not automatically attached. If you want to use rgl functions, you must either prefix commands with rgl:: or call library(rgl) in your session.

Function ordirgl is simalar as 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 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.

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 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.

There are obvious ways of improving the function. Contributions are welcome.