ordiarrows: 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 levels and replicates 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.

Examples

Run this code

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))

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