Description Usage Arguments Details Value Warning Author(s) See Also Examples
Function ordiplot3d
displays threedimensional ordination
graphics using scatterplot3d
. Function
works with all ordination results form vegan and all ordination
results known by scores
function.
1 2 3  ordiplot3d(object, display = "sites", choices = 1:3, col = "black",
ax.col = "red", arr.len = 0.1, arr.col = "blue", envfit,
xlab, ylab, zlab, ...)

object 
An ordination result or any object known by

display 
Display 
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

arr.col 
Colour of biplot 
envfit 
Fitted environmental variables from 
xlab, ylab, zlab 
Axis labels passed to

... 
Other parameters passed to graphical functions. 
Function ordiplot3d
plots static threedimensional 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
twodimensional 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 nonconstrained 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).
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 threedimensional coordinates onto
the plane used in the current plot (see Examples). In addition,
there is a function envfit.convert
that projects a
threedimensional envfit
object to the current plot.
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
.
Jari Oksanen
scatterplot3d
,
ordiplot
, ordiarrows
,
ordihull
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32  ### 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))

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.44
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
3: .onUnload failed in unloadNamespace() for 'rgl', details:
call: fun(...)
error: object 'rgl_quit' not found
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