ordixyplot {vegan} | R Documentation |

Functions `ordicloud`

, `ordisplom`

and `ordixyplot`

provide an interface to plot ordination results using Trellis
functions `cloud`

, `splom`

and `xyplot`

in package lattice.

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", ...)

`x` |
An ordination result that `scores` knows: any
ordination result in vegan and many others. |

`data` |
Optional data to amend ordination results. The ordination
results are found from `x` , but you may give here data for other
variables needed in plots. Typically these are environmental data. |

`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
`ordisplom` , special character `.` refers to the
ordination result. |

`display` |
The kind of scores: an argument passed to
`scores` . |

`choices` |
The axes selected: an argument passed to
`scores` . |

`panel, prepanel` |
The names of the panel and prepanel functions. |

`aspect` |
The aspect of the plot (passed to the lattice function). |

`envfit` |
Result of `envfit` function displayed in
`ordixyplot` . Please note that this needs same `choices`
as `ordixyplot` . |

`type` |
The type of plot. This knows the same alternatives as
`panel.xyplot` . In addition `ordixyplot`
has alternatives `"biplot"` and `"arrows"` . The first
displays fitted vectors and
factor centroids of `envfit` , or in constrained ordination, the
biplot arrows and factor centroids if `envfit` is not
given. The second (`type = "arrows"` ) is a trellis variant of
`ordiarrows` and draws arrows by `groups` . The
line parameters are controlled by
`trellis.par.set` for `superpose.line` ,
and the user can set `length` , `angle` and `ends`
parameters of `panel.arrows` . |

`...` |
Arguments passed to `scores` methods or
lattice functions. |

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
non-isometric scaling of graphs. You cannot select isometric scaling
in `ordisplom`

.

The function return `Lattice`

objects of class
`"trellis"`

.

Jari Oksanen

`Lattice`

,
`xyplot`

,
`splom`

,
`cloud`

,
`panel.splom`

,
`panel.cloud`

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"))

[Package *vegan* version 1.16-32 Index]