Three-Dimensional Ordination Graphics
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.
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 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).
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.
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
### 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))
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