R: Trellis (Lattice) Plots for Ordination

ordixyplot {vegan} | R Documentation

## 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

    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 `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.

### 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 non-isometric 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

    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 = "symmetric")
    ## ... 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 2.4-3 Index]