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.

---

Three-Dimensional Ordination Graphics

Description

Function ordiplot3d displays three-dimensional ordination graphics using scatterplot3d. Function works with all ordination results form vegan and all ordination results known by scores function.

Usage

ordiplot3d(object, display = "sites", choices = 1:3, col = "black",
    ax.col = "red", arr.len = 0.1, arr.col = "blue", envfit,
    xlab, ylab, zlab, ...)

Arguments

object	An ordination result or any object known by scores.
display	Display "sites" or "species" or other ordination object recognized by scores.
choices	Selected three axes.
col	Colours of points. Can be a vector, and factors are interpreted as their internal numerical codes.
ax.col	Axis colour (concerns only the crossed axes through the origin).
arr.len	'Length' (width) of arrow head passed to arrows function.
arr.col	Colour of biplot arrows and centroids of environmental variables.
envfit	Fitted environmental variables from envfit displayed in the graph.
xlab, ylab, zlab	Axis labels passed to scatterplot3d. If missing, labels are taken from the ordination result. Set to NA to suppress labels.
...	Other parameters passed to graphical functions.

Details

Function ordiplot3d plots static three-dimensional scatter diagrams using scatterplot3d. Function uses most default settings of underlying graphical functions, and you must consult their help pages to change graphics to suit your taste (see scatterplot3d).

Function returns invisibly an object of class ordiplot3d which inherits from ordiplot. The result object contains the projected coordinates of plotted items and functions to convert 3D data to 2D (see scatterplot3d). Function will display only one selected set of scores, typically either "sites" or "species". Examples show how to use the invisible return object to add another set of points to the projected plot.

In constrained ordination (cca, rda, capscale), biplot arrows and centroids are always displayed similarly as in two-dimensional plotting function plot.cca. Alternatively, it is possible to display fitted environmental vectors or class centroids from envfit. These are displayed similarly as the results of constrained ordination, and they can be shown only for non-constrained ordination. The user must remember to specify at least three axes in envfit if the results are used with these functions.

The function has a scores method to extract the projected coordinates from the invisible return object. Standard vegan functions can be used with the returned object. You can use any function from the ordihull and ordiarrows families (see Examples).

Value

Function ordiplot3d returns invisibly an object of class "ordiplot3d" inheriting from ordiplot. The return object will contain the coordinates projected onto two dimensions for points, and the projected coordinates of origin, and possibly the projected coordinates of the heads of arrows and centroids of environmental variables. The result will also contain the object returned by scatterplot3d, including function xyz.convert which projects three-dimensional coordinates onto the plane used in the current plot (see Examples). In addition, there is a function envfit.convert that projects a three-dimensional envfit object to the current plot.

Warning

Please note that scatterplot3d sets internally some graphical parameters (such as mar for margins) and does not honour default settings. It is advisable to study carefully the documentation and examples of scatterplot3d.

Author(s)

Jari Oksanen

See Also

scatterplot3d, ordiplot, ordiarrows, ordihull.

Examples

### Default 'ordiplot3d'
data(dune, dune.env)
ord <- cca(dune ~ A1 + Moisture, dune.env)
ordiplot3d(ord)
### A boxed 'pin' version
ordiplot3d(ord, type = "h")
### More user control
pl <- ordiplot3d(ord, scaling = "symmetric", angle=15, type="n")
points(pl, "points", pch=16, col="red", cex = 0.7)
### identify(pl, "arrows", col="blue") would put labels in better positions
text(pl, "arrows", col="blue", pos=3)
text(pl, "centroids", col="blue", pos=1, cex = 1)
### Add species using xyz.convert function returned by ordiplot3d
sp <- scores(ord, choices=1:3, display="species", scaling="symmetric")
text(pl$xyz.convert(sp), rownames(sp), cex=0.7, xpd=TRUE)
### Two ways of adding fitted variables to ordination plots
ord <- cca(dune)
ef <- envfit(ord ~ Moisture + A1, dune.env, choices = 1:3)
### 1. use argument 'envfit'
ordiplot3d(ord, envfit = ef)
### 2. use returned envfit.convert function for better user control
pl3 <- ordiplot3d(ord)
plot(pl3$envfit.convert(ef), at = pl3$origin)
### envfit.convert() also handles different 'choices' of axes
pl3 <- ordiplot3d(ord, choices = c(1,3,2))
plot(pl3$envfit.convert(ef), at = pl3$origin)
### vegan::ordiXXXX functions can add items to the plot
ord <- cca(dune)
pl4 <- with(dune.env, ordiplot3d(ord, col = Management, pch=16))
with(dune.env, ordiellipse(pl4, Management, draw = "poly", col = 1:4,
  alpha = 60))
with(dune.env, ordispider(pl4, Management, col = 1:4, label = TRUE))

---

Three-Dimensional Dynamic Ordination Graphics

Description

Function ordirgl displays three-dimensional dynamic ordination graphs which can be rotated and zoomed. This function works with all ordination results from vegan and all ordination results known by the scores function. The orgl-prefixed functions add elements to the ordirgl graph similarly as ordi-prefixed functions in vegan.

Usage

ordirgl(object, display = "sites", choices = 1:3, type = "p", col = "black",
    ax.col = "red", arr.col = "yellow", radius, text, envfit, ...)
orglpoints(object, display = "sites", choices = 1:3, radius, col = "black", ...)
orgltext(object, text, display = "sites", choices = 1:3, adj = 0.5,
    col = "black", ...)
orglsegments(object, groups, order.by, display = "sites", choices = 1:3,
    col = "black", ...)
orglspider(object, groups, display = "sites", w = weights(object, display),
    choices = 1:3, col = "black", ...)
orglellipse(object, groups, display = "sites", w = weights(object, display),
    kind = c("sd", "se", "ehull"), conf, choices = 1:3, alpha = 0.3,
    col = "red", ...)
orglspantree(object, spantree, display = "sites", choices = 1:3,
    col = "black", ...)
orglcluster(object, cluster, prune = 0, display = "sites", choices = 1:3,
    col = "black", ...)

Arguments

object	An ordination result or any object known by scores.
display	Display "sites" or "species" or other ordination object recognized by scores.
choices	Selected three axes.
type	The type of plots: "p" for points or "t" for text labels.
ax.col	Axis colour (concerns only the crossed axes through the origin).
arr.col	Colour of biplot arrows and centroids of environmental variables.
radius	Size of points in the units of ordination scores.
text	Text to override the default with type = "t".
envfit	Fitted environmental variables from envfit displayed in the graph. Use envfit = NA to suppress display of environmental variables in constrained ordination.
adj	Text justification passed to text3d.
groups	Factor giving the groups for which the graphical item is drawn.
order.by	Order points by this variable within groups.
w	Weights used to find the average within group. Weights are used automatically for cca and decorana results, unless undone by the user. w=NULL sets equal weights to all points.
kind	Draw ellipse for standard deviations of points ("sd") or standard deviations of their averages ("se") or an ellipsoid hull enclosing all points in the group ("ehull".
conf	Confidence limit for ellipses, e.g., 0.95. If not given, sd or se ellipses are drawn.
col	Colour of items. This can be a vector and factors are interpreted as their internal numerical values. If the function has a groups argument, vector col is used for each of these, and for other functions it is matched to points in ordirgl (see Details below).
alpha	Transparency of colour between 0.0 (fully transparent) and 1.0 (non-transparent).
spantree	A minimum spanning tree object from vegan spantree.
cluster	Result of hierarchic cluster analysis, such as hclust or agnes.
prune	Number of upper levels hierarchies removed from the tree. If prune > 0, tree will be cut into prune + 1 disconnected trees.
...	Other parameters passed to graphical functions.

Details

Function ordirgl plots dynamic graphics using OpenGL with the rgl package. It clears the graphics device and starts a new plot. The function was designed for ordination methods in the vegan package, but it can handle any method known to vegan scores function, or to any three column matrix. The orgl-prefixed functions add items to the opened rgl graphics device.

Function ordirgl uses most default settings of underlying graphical functions in rgl. It plots only one set of points, but functions orglpoints and orgltext can add new items to an existing plot. The points are plotted using spheres3d and the text using texts3d which both have their own configuration switches and their general look and feel can be modified with material3d. The point size is directly defined by radius argument in the units of ordination scores in spheres3d, but ordirgl uses a default size of 1% of the length of the longest axis, and this can be further modified by the cex multiplier.

In constrained ordination (cca, rda, capscale), biplot arrows and centroids are always displayed similarly as in two-dimensional plotting function plot.cca. Alternatively, it is possible to display fitted environmental vectors or class centroids from envfit in both graphs. These are displayed similarly as the results of constrained ordination, and they can be shown only for non-constrained ordination. The user must remember to specify at least three axes in envfit if the results are used with these functions.

Function orglsegments is similar to vegan ordisegments and connects points by line segments. This can be useful for regular transects. The colour of segments can be a vector which corresponds to the groups and will be recycled.

Function orglspider is similar as vegan ordispider: it connects points to their weighted centroid within "groups", and in constrained ordination it can connect "wa" or weighted averages scores to corresponding "lc" or linear combination scores if "groups" is missing. Function orglellipse is similar as vegan ordiellipse and draws ellipsoids of standard deviance, standard error or confidence regions for groups. At least four points are needed to define an ellipsoid in 3D, and even these will fail if all points are strictly on 2D. The col argument for both of these functions can be a vector corresponding to the groups.

Function orglspantree adds a minimum spanning tree from vegan spantree. This a 3D equivalent of lines.spantree. Function orglcluster adds a hierarchic cluster tree from hclust or related functions. This is a 3D equivalent of ordicluster. The col argument for both of these functions can be a vector corresponding to the connected points. In orglspantree the line colour is a mixture of colours of joined points, and in orglcluster it is a mixture of all points in the cluster.

Value

Function ordirgl returns nothing.

Warning

Function ordirgl uses OpenGL package rgl which may not be functional in all platforms.

Author(s)

Jari Oksanen

See Also

rgl, spheres3d, text3d, rgl.viewpoint, envfit. These are 3D dynamic variants of vegan functions ordiplot, ordisegments, ordispider and ordiellipse, ordicluster and lines.spantree.

Examples

if (interactive() && require(rgl, quietly = TRUE)) {
data(mite, mite.env)
ord <- rda(decostand(mite, "hellinger"))
ordirgl(ord, size=4, col = "yellow")
orgltext(ord, display = "species")
## show groups of Shrub abundance
## ordirgl: col by points
with(mite.env, ordirgl(ord, col = as.numeric(Shrub), scaling = "sites"))
## orglspider & orglellipse: col by groups
with(mite.env, orglspider(ord, Shrub, col = 1:3, scaling = "sites"))
with(mite.env, orglellipse(ord, Shrub, col = 1:3, kind = "se", conf = 0.95,
    scaling = "sites"))
}

---

Ordination Plot with Movable Labels

Description

Function orditkplot produces an editable ordination plot with points and labels. The labels can be moved with mouse, and the edited plot can be saved as an encapsulated postscript file or exported via R plot function to other graphical formats, or saved in the R session for further processing.

Usage

orditkplot(x, display = "species", choices = 1:2, width, xlim, ylim, 
   tcex = 0.8, tcol, pch = 1,  pcol, pbg, pcex = 0.7, labels,  ...)
## S3 method for class 'orditkplot'
plot(x, ...)
## S3 method for class 'orditkplot'
points(x, pch = x$args$pch, cex = x$args$pcex,
       col = x$args$pcol, bg = x$args$pbg, ...)
## S3 method for class 'orditkplot'
text(x, cex = x$args$tcex, col = x$args$tcol,
     font = attr(x$labels, "font"), ...)
## S3 method for class 'orditkplot'
scores(x, display, ...)

Arguments

x	An ordination result or any other object that scores can handle, or for the plot function the object dumped from the interactive orditkplot session.
display	Type of scores displayed. For ordination scores this typically is either "species" or "sites", and for orditkplot result it is either "points" or "labels".
choices	Axes displayed.
width	Width of the plot in inches; defaults to the current width of the graphical device.
xlim, ylim	x and y limits for plots: points outside these limits will be completely removed.
tcex	Character expansion for text labels.
tcol	Colour of text labels.
pch, pcol, pbg	Point type and outline and fill colours. Defaults pcol="black" and pbg="transparent". Argument pbg has an effect only in filled plotting characters pch = 21 to 25.
pcex	Expansion factor for point size.
labels	Labels used instead of row names.
cex, col, bg, font	graphical parameters used in the points and text methods. See par.
...	Other arguments passed to the function. These can be graphical parameters (see par) used in the plot, or extra arguments to scores. These arguments are ignored in plot, but honoured in text and points.

Details

Function orditkplot uses tcltk package to draw Tcl/Tk based ordination graphics with points and labels. The function opens an editable canvas with fixed points, but the labels can be dragged with mouse to better positions or edited. In addition, it is possible to zoom to a part of the graph.

The function knows the following mouse operations:

• Left mouse button can be used to move labels to better positions. A line will connect a label to the corresponding point.

• Double clicking left mouse button opens a window where the label can be edited. After editing the label, hit the Return key.

• Right mouse button (or alternatively, Shift-Mouse button with one-button mouse) can be used for zooming to a part of the graph. Keeping the mouse button down and dragging will draw a box of the zoomed area, and after releasing the button, a new plot window will be created (this is still preliminary: all arguments are not passed to the new plot).

In addition there are buttons for the following tasks: Copy to EPS copies the current plot to an encapsulated postscript (eps) file using standard Tcl/Tk utilities. The faithfulness of this copy is system dependent. Button Export plot uses plot.orditkplot function to redraw the plot into graphical file formats. Depending on the system, the following graphical formats may be available: eps, pdf, svg, png, jpeg, tiff, bmp or xfig. Some of the output formats may be edited with external software: svg files with Illustrator or Inkscape, and xfig with the legacy program XFig. Button Save to R writes the edited coordinates of labels and points to the R session for further processing, and the plot.orditkplot function can be used to display the results. For faithful replication of the plot, the graph must have similar dimensions as the orditkplot canvas had originally. The plot function cannot be configured, but it uses the same settings as the original Tcl/Tk plot. However, points and text functions are fully configurable, but use the stored defaults for consistency with plot.orditkplot if none are supplied. Finally, button Close closes the window.

The produced plot will have equal aspect ratio. The width of the horizontal axis is fixed, but vertical axes will be scaled to needed height, and you can use scrollbar to move vertically if the whole canvas does not fit the window. If you use dumped labels in ordinary R plots, your plot must have the same dimensions as the orditkplot canvas to have identical location of the labels.

The function only displays one set of scores. However, you can use ordipointlabel (vegan) to produce a result object that has different points and text types for several sets of scores and this can be further edited with orditkplot. For a good starting solution you need to scale the ordipointlabel result so that the points span over the whole horizontal axis. The function cannot show environmental variables or constraints, but it is limited to unconstrained ordination.

The plot is a Tcl/Tk canvas, but the function tries to replicate standard graphical device of the platform, and it honours several graphical parameters (see par). Many of the graphical parameters can be given on the command line, and they will be passed to the function without influencing other graphical devices in R. At the moment, the following graphical parameters are honoured: pch bg, cex, cex.axis, cex.lab, col (for labels), col.axis, col.lab, family (for font faces), fg, font, font.axis, font.lab, lheight, lwd (for the box), mar, mex, mgp, ps, tcl. These can be set with par, and they also will influence other plots similarly.

The tkcanvas text cannot be rotated, and therefore vertical axis is not labelled, and las parameter will not be honoured in the Tcl/Tk plot, but it will be honoured in the exported R plots and in plot.orditkplot.

Value

Function returns nothing useful directly, but you can save the edited graph to a file or save the edited positions to an R session for further processing and plotting.

Note

You need tcltk package and R must have been configured with capabilities for tcltk. Depending on your OS, you may need to start X11 and set the display before loading tcltk and starting the function (for instance, with Sys.setenv("DISPLAY"=":0")). See tcltk-package.

Author(s)

Jari Oksanen

See Also

Function ordipointlabel is an automatic procedure with similar goals of avoiding overplotting, and its output can be edited with orditkplot. See ordiplot, plot.cca, and orditorp for alternative ordination plots.

Examples

if(interactive() && capabilities("tcltk")) {
data(varespec)
ord <- cca(varespec)
## Do something with the graph and end by clicking "Dismiss"
orditkplot(ord, mar = c(4,4,1,1)+.1, font=3)
## Use ordipointlabel to produce a plot that has both species and site
## scores in different colors and plotting symbols
pl <- ordipointlabel(ord)
orditkplot(pl)
}

---

Draw Cluster Tree over a Plane

Description

Function draws a 3D plot where ordination result is at the bottom plane and a hclust dendrogram is drawn above the plane.

Usage

orditree3d(ord, cluster, prune = 0, display = "sites", choices = c(1, 2),
    col = "blue", text, type = "p", ...)
ordirgltree(ord, cluster, prune = 0, display = "sites", choices = c(1, 2),
    col = "blue", text, type = "p", ...)

Arguments

ord	An ordination object or an ordiplot object or any other structure defining a 2D plane.
cluster	Result of hierarchic cluster analysis, such as hclust or agnes or any other clutering that can be coerced to a compliant format by as.hclust.
prune	Number of upper levels hierarchies removed from the tree. If prune > 0, tree will be cut into prune + 1 disconnected trees.
choices	Choice of ordination axes.
display	Ordination scores displayed.
col	Colour of tree. The colour can be a vector and it is used for the points, text and terminal branches. The colour of internal branches is a mixture of connected leaves.
text	Text to replace the default of item labels when type = "t".
type	Display of leaves: "p" for points, "t" for text, and "n" for no display.
...	Arguments passed to scores and graphical functions.

Details

orditree3d uses scatterplot3d package to draw a static 3D plot of the dendrogram over the ordination, and ordirgltree uses rgl to make a dynamic, spinnable plot. The functions were developed to plot a cluster dendrogram over a 2D ordination plane, but any other plane can be used, for instance, a map.

Value

Function orditree3d returns invisibly a scatterplot3d result object amended with items points and internal that give the projected coordinates of ordination scores and internal nodes, and col.points and col.internal that give their colours. All matrix-like objects can be accessed with scores.

Function ordirgltree returns nothing.

Author(s)

Jari Oksanen.

See Also

orglcluster and ordicluster (in vegan).

Examples

data(dune, dune.env)
  d <- vegdist(dune)
  m <- metaMDS(d)
  cl <- hclust(d, "aver")
  orditree3d(m, cl, pch=16, col=cutree(cl, 3))
  ## ordirgltree makes ordinary rgl graphics. It accepts
  ## material3d() settings, and you can add elements to the
  ## open graph (for instance, bbox3d()).
  if (interactive() && require(rgl, quietly = TRUE)) {
  with(dune.env, ordirgltree(m, cl, col = as.numeric(Management), size = 6,
     lwd = 2, alpha = 0.6))
  }

---

Dynamic 3D plot of isomap ordination.

Description

Function displays a dynamic 3D plot from isomap ordination.

Usage

rgl.isomap(x, web = "white", ...)

Arguments

x	Result from isomap.
web	Colour of the web. If this is a vector matching the number of points, the colour of links is a mixture of joined points. NA skips drawing the web.
...	Other parameters passed to ordirgl and scores.

Details

Function rgl.isomap displays dynamic 3D plots that can be rotated on the screen. The functions is based on ordirgl, but it adds the connecting lines. The function passes extra arguments to scores or ordirgl functions so that you can select axes, or define colours and sizes of points.

Value

Function returns nothing.

Note

This is a support function for isomap ordination in the vegan package.

Author(s)

Jari Oksanen.

See Also

isomap, ordirgl, scores.

Examples

if (interactive() && require(rgl, quietly = TRUE)) {
data(BCI)
dis <- vegdist(BCI)
## colour points and links by the dominant species
dom <- factor(make.cepnames(names(BCI))[apply(BCI, 1, which.max)])
ord <- isomap(dis, k=3)
rgl.isomap(ord, col = as.numeric(dom), web = as.numeric(dom), lwd=2)
}

---

Dynamic Perspective Plot of Renyi Diversity Accumulation

Description

Function rgl.renyiaccum displays a dynamic 3D plot of the result of renyiaccum function in the vegan package. Function persp.renyiaccum (in vegan) produces similar static plots.

Usage

rgl.renyiaccum(x, rgl.height = 0.2, ...)

Arguments

x	A renyiaccum result.
rgl.height	Vertical scaling of the plot.
...	Other arguments passed to the function (ignored).

Details

This is a graphical support function to renyiaccum in vegan. Similar static plots can be produced by persp.renyiaccum.

Value

Function returns nothing.

Author(s)

Roeland Kindt.

See Also

renyiaccum, persp.renyiaccum, rgl.

Examples

if (interactive() && require(rgl, quietly = TRUE)){
data(BCI)
mod <- renyiaccum(BCI[1:12,])
persp(mod)
rgl.renyiaccum(mod)
}

---