Trellis (Lattice) Plots for Ordination
Description
Functions ordicloud
, ordisplom
and ordixyplot
provide an interface to plot ordination results using Trellis
functions cloud
, splom
and xyplot
in package lattice.
Usage
1 2 3 4 5 6 7  ordixyplot(x, data = NULL, formula, display = "sites", choices = 1:3,
panel = "panel.ordi", aspect = "iso", envfit,
type = c("p", "biplot"), ...)
ordisplom(x, data=NULL, formula = NULL, display = "sites", choices = 1:3,
panel = "panel.ordi", type = "p", ...)
ordicloud(x, data = NULL, formula, display = "sites", choices = 1:3,
panel = "panel.ordi3d", prepanel = "prepanel.ordi3d", ...)

Arguments
x 
An ordination result that 
data 
Optional data to amend ordination results. The ordination
results are found from 
formula 
Formula to define the plots. A default formula will be
used if this is omitted. The
ordination axes must be called by the same names as in the
ordination results (and these names vary among methods). In

display 
The kind of scores: an argument passed to

choices 
The axes selected: an argument passed to

panel, prepanel 
The names of the panel and prepanel functions. 
aspect 
The aspect of the plot (passed to the lattice function). 
envfit 
Result of 
type 
The type of plot. This knows the same alternatives as

... 
Arguments passed to 
Details
The functions provide an interface to the corresponding lattice
functions. All graphical parameters are passed to the lattice
function so that these graphs are extremely configurable. See
Lattice
and xyplot
,
splom
and cloud
for
details, usage and possibilities.
The argument x
must always be an ordination result. The scores
are extracted with vegan function scores
so that
these functions work with all vegan ordinations and many others.
The formula
is used to define the models. All functions have
simple default formulae which are used if formula
is missing.
If formula is omitted in ordisplom
it
produces a pairs plot of ordination axes and variables in
data
. If formula
is given, ordination results must be
referred to as .
and other variables by their names. In other
functions, the formula must use the names of ordination scores and names
of data
.
The ordination scores are found from x
, and data
is
optional. The data
should contain other variables than
ordination scores to be used in plots. Typically, they are
environmental variables (typically factors) to define panels or plot
symbols.
The proper work is done by the panel function. The layout can be
changed by defining own panel functions. See
panel.xyplot
,
panel.splom
and
panel.cloud
for details and survey of
possibilities.
Ordination graphics should always be isometric: same scale should be
used in all axes. This is controlled (and can be changed) with
argument aspect
in ordixyplot
. In ordicloud
the
isometric scaling is defined in panel
and prepanel
functions. You must replace these functions if you want to have
nonisometric scaling of graphs. You cannot select isometric scaling
in ordisplom
.
Value
The function return Lattice
objects of class
"trellis"
.
Author(s)
Jari Oksanen
See Also
Lattice
,
xyplot
,
splom
,
cloud
,
panel.splom
,
panel.cloud
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20  data(dune)
data(dune.env)
ord < cca(dune)
## Pairs plots
ordisplom(ord)
ordisplom(ord, data=dune.env, choices=1:2)
ordisplom(ord, data=dune.env, form = ~ .  Management, groups=Manure)
## Scatter plot
ordixyplot(ord, data=dune.env, form = CA1 ~ CA2  Management,
groups=Manure)
## Choose a different scaling
ordixyplot(ord, scaling = 3)
## ... Slices of third axis
ordixyplot(ord, form = CA1 ~ CA2  equal.count(CA3, 4), type = c("g","p"))
## Display environemntal variables
ordixyplot(ord, envfit = envfit(ord ~ Management + A1, dune.env, choices=1:3))
## 3D Scatter plots
ordicloud(ord, form = CA2 ~ CA3*CA1, groups = Manure, data = dune.env)
ordicloud(ord, form = CA2 ~ CA3*CA1  Management, groups = Manure,
data = dune.env, auto.key = TRUE, type = c("p","h"))
