ordipointlabel {vegan} | R Documentation |

The function `ordipointlabel`

produces ordination plots with
points and text label to the points. The points are in the exact
location given by the ordination, but the function tries to optimize
the location of the text labels to minimize overplotting text. The
function may be useful with moderately crowded ordination plots.

ordipointlabel(x, display = c("sites", "species"), choices = c(1, 2), col = c(1, 2), pch = c("o", "+"), font = c(1, 1), cex = c(0.8, 0.8), add = FALSE, select, ...) ## S3 method for class 'ordipointlabel' plot(x, ...)

`x` |
For |

`display` |
Scores displayed in the plot. |

`choices` |
Axes shown. |

`col, pch, font, cex` |
Colours, point types, font style and
character expansion for each kind of scores displayed in the
plot. These should be vectors of the same length as the number of
items in |

`add` |
Add to an existing plot. |

`select` |
Items to be displayed. This can either be a logical
vector which is |

`...` |
Other arguments passed to |

The function uses simulated annealing (`optim`

,
`method = "SANN"`

) to optimize the location of the text labels
to the points. There are eight possible locations: up, down, sides
and corners. There is a weak preference to text right above the
point, and a weak avoidance of corner positions. The exact locations
and the goodness of solution varies between runs, and there is no
guarantee of finding the global optimum. The optimization can take a
long time in difficult cases with a high number of potential
overlaps. Several sets of scores can be displayed in one plot.

The function is modelled after `pointLabel`

in
maptools package (which has chained dependencies of `S4`

packages).

The function returns invisibly an object of class
`ordipointlabel`

with items `xy`

for coordinates of
points, `labels`

for coordinates of labels, items `pch`

,
`cex`

and `font`

for graphical parameters of each point or
label. In addition, it returns the result of `optim`

as
an attribute `"optim"`

. The unit of overlap is the area
of character `"m"`

, and with variable `cex`

it is the
smallest alternative.

There is a `plot`

method based on `orditkplot`

but which
does not alter nor reset the graphical parameters via `par`

.

The result object from `ordipointlabel`

inherits from
`orditkplot`

, and can also be replotted with its
`plot`

method. It may be possible to further edit the result
object with `orditkplot`

, but for good results it is
necessary that the points span the whole horizontal axis without empty
margins.

The function is designed for ordination graphics, and the optimization works properly with plots of isometric aspect ratio.

Jari Oksanen

See `pointLabel`

for references.

`pointLabel`

for the model
implementation, and `optim`

for the optimization.

data(dune) ord <- cca(dune) plt <- ordipointlabel(ord) ## set scaling - should be no warnings! ordipointlabel(ord, scaling = 1) ## plot then add plot(ord, scaling = 3, type = "n") ordipointlabel(ord, display = "species", scaling = 3, add = TRUE) ordipointlabel(ord, display = "sites", scaling = 3, add = TRUE) ## redraw plot without rerunning SANN optimisation plot(plt)

[Package *vegan* version 2.0-10 Index]