plot.rdaTest {rdaTest}R Documentation

Canonical redundancy analysis triplots

Description

Function plot.rdaTest produces triplots from the output list of rdaTest.

Usage

## S3 method for class 'rdaTest':
plot (x, xax=1, yax=2, scaling=1, graph.type="notchosen", plot.sites=TRUE, 
plot.spe=TRUE, plot.env=TRUE, binary=NULL, height=6, width=6, xlim=NULL, 
ylim=NULL, ell=NULL, alpha=0.95, ell.axis=FALSE, mul.spe=0.8, mul.env=0.90, 
mul.text=0.10, pos.ell=NULL, pos.bin=NULL, pos.sites=1, label.sites=TRUE, 
label.spe=TRUE, label.env=TRUE, label.ell=TRUE, col.env="blue", col.spe="red", 
col.site="black", col.ell="black", lty.env=1, lty.spe=1, lty.ell=1, lty.axis=2, 
cex=1, cex.lab=1, cex.axis=1, lwd=1, len=0.1, saveplot=FALSE, path=NULL, 
mar.perc=NULL, interior.mar.perc=0.05, select.spe=NULL, ...)

Arguments

********** General plotting parameters
x The rdaTest output object. The most simple call to this function is to provide only the output object name of function rdaTest. Ex.: plot.rdaTest(toto) or plot(toto).
xax, yax Canonical axes that will be used for the triplot. These value can be negative; if so, the plot axes will be reversed.
scaling Allows the user to choose between the two scaling types, 1 or 2, for the triplots: scaling = 1: distance triplot (default); scaling = 2: correlation triplot.
graph.type Either "F" or "Z" – "F"= site scores, "Z" = fitted site scores.
plot.sites If TRUE, the sites will be plotted as small circles.
plot.spe If TRUE, the species (or other response variables) will be plotted.
plot.env If TRUE, the explanatory (environmental) variables will be plotted.
binary A vector specifying which of the environmental variables are binary; the corresponding data points will be averaged and represented by a symbol instead of an arrow, as in Canoco.
saveplot If saveplot = FALSE, the graph will only appear in a window (quartz). If saveplot = TRUE, no graph will be plotted on the screen; a pdf file will created instead.
path Complete path to the file in which the plot will be saved; example: ~/Desktop/toto.pdf
width, height Size of the triplot in inches.
xlim, ylim Vectors describing the minimum and maximum values of the plotted region.
lwd Line width for the axes, arrows, and ellipses.
len Length of the arrow heads.
mar.perc Allows one to increase or decrease the size of the outer margin of the graph, using a fraction of the total width and height of the graph; the value must be between 0 and 1.
interior.mar.perc Allows one to increase the interior margin of the plot, i.e. the space between the outermost points and the frame, using a fraction of the total size of the frame; the value must be between 0 and 1. Default value: interior.mar.perc=0.05.
select.spe Vector containing a selection of the species, to be drawn in the biplot. Draw all species if select.spe=NULL (default value).
... Other graphical arguments passed to the function.
**********
********** Parameters controlling the confidence ellipses around groups of points
ell Draw confidence ellipses around groups of points according to a vector defining the group assignments of the objects; see section Examples below.
alpha Confidence region of the ellipses (e.g. 0.90, 0.80, etc.) Default value: 0.95.
lty.ell Drawing type for ellipses; see lty in the help documentation file of par.
col.ell The ellipses and group identification text color; see lty in the help file of par.
ell.axis If TRUE, draw the major and minor axes of the ellipses.
pos.ell Offset the group names relative to the ellipse centers: 1=bottom, 2=left, 3=top, 4=right.
**********
********** Parameters for arrows and text
label.sites If TRUE, labels are added to the site symbols.
label.spe If TRUE, labels are added to the species arrows.
label.env If TRUE, labels are added to the environmental variable arrows.
label.ell If TRUE, labels (numbers) are added to the group ellipses.
col.env Color for the environmental variable arrows and text.
col.spe Color for the species arrows and text.
col.site Color for the site points and text.
lty.env Environmental variable arrows drawing type. See lty in the help documentation file of par.
lty.spe Species arrows drawing type. See lty in the help documentation file of par.
lty.axis Drawing type for axes, full lines, dotted lines, etc.
cex A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default. See lty in the help documentation file of par.
cex.lab Change to the font size of the site, species, and environmental variable labels, with respect to a standard of 1.
cex.axis Change to the font size of the axis labels, with respect to a standard of 1.
mul.spe Multiplier based on the range of the plot axes, which changes to the length of the species arrows proportionally; 1 = maximum relative length in the set of arrows.
mul.env Same, for the explanatory variables.
mul.text Text position at the end of each arrow plus a percentage; default is 10 percent.
pos.bin Offset the names of the binary variables: 1=bottom, 2=left, 3=top, 4=right.
pos.sites Offset the site labels: 1=bottom, 2=left, 3=top, 4=right.

Details

A triplot of the results of the canonical redundancy analysis (RDA) is drawn using either scaling 1 or scaling 2.

Scaling type 1 triplot uses matrices Z or F for objects and U for variables; notation as in Legendre and Legendre (1998, Section 11.1.1). This projection preserves the Euclidean distances among the objects.

Scaling type 2 triplot uses matrices ZSc2 or FSc2 for objects and USc2 for variables. This projection preserves the correlations among the response variables' fitted values.

Author(s)

Sebastien Durand and Pierre Legendre, Universite de Montreal

References

Aart, P. J. M. (van der) and N. Smeenk-Enserink. 1975. Correlations between distributions of hunting spiders (Lycosidae, Ctenidae) and environmental characteristics in a dune area. Neth. J. Zool. 25: 1-45.

Legendre, P. and Legendre, L. 1998. Numerical Ecology. 2nd English ed. Elsevier, Amsterdam.

See Also

rdaTest

Examples

## Analysis of Table 11.3 of Legendre and Legendre (1998, p. 590)  
data(Table.11.3)
Y = Table.11.3[,1:6]
X = Table.11.3[,7:10]
result = rdaTest(Y, X, test.F=TRUE, nperm=999)
plot(result, graph.type="Z")

## Draw 3 species only in the biplot
vec = c(1,3,6)
plot(result, graph.type="Z", select.spe=vec)

## Reverse orientation of abscissa (parameter xax) in the plot
plot(result, xax=-1, yax=2, mul.spe=0.90, mul.env=0.70, mul.text=0.10, 
scaling=1, graph.type="F", mai.perc=0.15, pos.sites=3) 

## Draw confidence ellipses around groups of points, spider data 
## (Aart and Smeenk-Enserink, 1975)
data(spiders.spe)
data(spiders.env) 
# Hellinger transformation of the species abundance data prior to RDA
library(vegan)
spiders.hel = decostand(spiders.spe, "hellinger")
result.spiders = rdaTest(spiders.hel, spiders.env, test.F=TRUE, nperm=999)
# Vector vec divides the sites into three a priori groups
vec = c(2,1,2,1,1,3,1,3,2,2,2,2,1,3,3,3,3,3,3,3,3,2,2,2,3,2,2,2)
plot(result.spiders, graph.type="Z", ell=vec, lty.ell=3, pos.sites=4, 
mar.perc=0.15)

## Plot the sites and environmental variables, but not the species
plot(result.spiders, graph.type="Z", plot.spe=FALSE, ell=vec, lty.ell=3, 
pos.sites=4, mar.perc=0.15)

[Package rdaTest version 1.7 Index]