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 |
groups |
Factor giving the groups for which the graphical item is drawn. |
levels , replicates |
Alternatively, regular
groups can be defined with arguments |
order.by |
Order points by increasing order of this variable
within |
display |
Item to displayed. |
show.groups |
Show only given groups. This can be a vector, or
|
label |
Label the |
startmark |
plotting character used to mark the first item. The
default is to use no mark, and for instance, |
col |
Colour of lines, |
length |
Length of edges of the arrow head (in inches). |
lty , lwd |
Line type, line width used for
|
... |
Parameters passed to graphical functions such as
|
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))