R: Add Arrows and Line Segments to Ordination Diagrams

ordiarrows {vegan} | R Documentation

## Add Arrows and Line Segments to Ordination Diagrams

### Description

Functions to add arrows, line segments, regular grids of points. The ordination diagrams can be produced by `vegan` `plot.cca`, `plot.decorana` or `ordiplot`.

### Usage

    ordiarrows(ord, groups, levels, replicates, order.by, display = "sites",
             col = 1, show.groups, startmark, label = FALSE, length = 0.1, ...)
    ordisegments(ord, groups, levels, replicates, order.by, display = "sites",
             col = 1, show.groups, label = FALSE, ...)
    ordigrid(ord, levels, replicates, display = "sites",  lty = c(1,1),
             col = c(1,1), lwd = c(1,1), ...)

### Arguments

`ord` | An ordination object or an `ordiplot` object.
`groups` | Factor giving the groups for which the graphical item is drawn.
`levels, replicates` | Alternatively, regular groups can be defined with arguments `levels` and `replicates`, where `levels` gives the number of groups, and `replicates` the number of successive items at the same group.
`order.by` | Order points by increasing order of this variable within `groups`. Reverse sign of the variable for decreasing ordering.
`display` | Item to displayed.
`show.groups` | Show only given groups. This can be a vector, or `TRUE` if you want to show items for which condition is `TRUE`. This argument makes it possible to use different colours and line types for groups. The default is to show all groups.
`label` | Label the `groups` by their names. In `ordiellipse`, `ordihull` and `ordispider` the the group name is in the centroid of the object, in `ordiarrows` in the start of the arrow, and in `ordisegments` at both ends. `ordiellipse` and `ordihull` use standard `text`, and others use `ordilabel`.
`startmark` | plotting character used to mark the first item. The default is to use no mark, and for instance, `startmark = 1` will draw a circle. For other plotting characters, see `pch` in `points`.
`col` | Colour of lines, `label` borders and `startmark` in `ordiarrows` and `ordisegments`. This can be a vector recycled for `groups`. In `ordigrid` it can be a vector of length 2 used for `levels` and `replicates`.
`length` | Length of edges of the arrow head (in inches).
`lty, lwd` | Line type, line width used for `level`s and `replicate`s in `ordigrid`.
`...` | Parameters passed to graphical functions such as `lines`, `segments`, `arrows`, or to `scores` to select axes and scaling etc.

### Details

Function `ordiarrows` draws `arrows` and `ordisegments` draws line `segments` between successive items in the groups. Function `ordigrid` draws line `segments` both within the groups and for the corresponding items among the groups.

### Note

These functions add graphical items to ordination graph: You must draw a graph first.

### Author(s)

Jari Oksanen

### See Also

The functions pass parameters to basic graphical functions, and you may wish to change the default values in `arrows`, `lines` and `segments`. You can pass parameters to `scores` as well.

### Examples

    example(pyrifos)
    mod <- rda(pyrifos)
    plot(mod, type = "n")
    ## Annual succession by ditches, colour by dose
    ordiarrows(mod, ditch, label = TRUE, col = as.numeric(dose))
    legend("topright", levels(dose), lty=1, col=1:5, title="Dose")
    ## Show only control and highest Pyrifos treatment
    plot(mod, type = "n")
    ordiarrows(mod, ditch, label = TRUE,
       show.groups = c("2", "3", "5", "11"))
    ordiarrows(mod, ditch, label = TRUE, show = c("6", "9"),
       col = 2)
    legend("topright", c("Control", "Pyrifos 44"), lty = 1, col = c(1,2))

[Package vegan version 2.4-3 Index]