Description Usage Arguments Details Value Warning Author(s) See Also Examples
Function ordirgl
displays threedimensional 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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16  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", ...)

object 
An ordination result or any object known by 
display 
Display 
choices 
Selected three axes. 
type 
The type of plots: 
ax.col 
Axis colour (concerns only the crossed axes through the origin). 
arr.col 
Colour of biplot 
radius 
Size of points in the units of ordination scores. 
text 
Text to override the default with 
envfit 
Fitted environmental variables from 
adj 
Text justification passed to 
groups 
Factor giving the groups for which the graphical item is drawn. 
order.by 
Order points by this variable within 
w 
Weights used to find the average within group. Weights are
used automatically for 
kind 
Draw ellipse for standard deviations of points
( 
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 
alpha 
Transparency of colour between 0.0 (fully transparent) and 1.0 (nontransparent). 
spantree 
A minimum spanning tree object from vegan

cluster 
Result of hierarchic cluster analysis, such as

prune 
Number of upper levels hierarchies removed from the
tree. If 
... 
Other parameters passed to graphical functions. 
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
rgl.spheres
and the text using
rgl.texts
which both have their own configuration
switches and their general look and feel can be modified with
rgl.material
. The point size is directly defined
by radius
argument in the units of ordination scores in
rgl.spheres
, 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
twodimensional 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 nonconstrained
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.
Function ordirgl
returns nothing.
Function ordirgl
uses OpenGL package rgl
which may not be functional in all platforms.
Jari Oksanen
rgl
, rgl.spheres
,
rgl.texts
, rgl.viewpoint
,
envfit
. These are 3D dynamic variants of
vegan functions ordiplot
,
ordisegments
, ordispider
and ordiellipse
,
ordicluster
and
lines.spantree
.
1 2 3 4 5 6 7 8 9 10 11 12 13  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"))
}

Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.