Trellis (Lattice) Plots for Ordination
provide an interface to plot ordination results using Trellis
xyplot in package lattice.
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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", ...)
An ordination result that
Optional data to amend ordination results. The ordination
results are found from
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
The kind of scores: an argument passed to
The axes selected: an argument passed to
The names of the panel and prepanel functions.
The aspect of the plot (passed to the lattice function).
The type of plot. This knows the same alternatives as
Arguments passed to
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
details, usage and possibilities.
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.
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
produces a pairs plot of ordination axes and variables in
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
The ordination scores are found from
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
The proper work is done by the panel function. The layout can be
changed by defining own panel functions. See
panel.cloud for details and survey of
Ordination graphics should always be isometric: same scale should be
used in all axes. This is controlled (and can be changed) with
isometric scaling is defined in
functions. You must replace these functions if you want to have
non-isometric scaling of graphs. You cannot select isometric scaling
The function return
Lattice objects of class
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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"))
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