Plots for symmetric co-correspondence analysis

Produces plots of the response and predictor from the results of a symmetric co-correspondence analysis.

# S3 method for symcoca
plot(x,
    which = "response",
    choices = 1:2,
    display = c("species", "sites"),
    scaling = FALSE,
    type,
    xlim = NULL,
    ylim = NULL,
    main = "",
    sub = "",
    ylab, xlab,
    ann = par("ann"),
    axes = TRUE,
    ...)

Arguments

x

an object of class "symcoca", the result of a call to symcoca.
which

character; should the response or predictor scores be plotted.
choices

a vector of length 2 indicating which predictive CoCA axes to plot.
display

which sets of scores are drawn. See scores.symcoca.
scaling

logical, whether scaling should be applied. See scores.symcoca.
type

one of "points", "text", or "none". Determines how the site and species scores are displayed. If type = "points", scores are plotted as points. If type = "text", then the row names of the scores matrices are plotted. If type = "none", then the scores are not plotted.
xlim, ylim

limits for the x and y axes. If non supplied, suitable limits will be determined from the data.
xlab, ylab

labels for the x and y axes. If non supplied suitable labels are formed from the result object.
main, sub

the main and sub titles for the plot.
ann

logical, if TRUE plots are annotated and not if FALSE, currently ignored.
axes

a logical value indicating whether both axes should be drawn on the plot.
...

other graphical parameters as in 'par' may also be passed as arguments.

References

Ter Braak, C.J.F and Schaffers, A.P. (2004) Co-Correspondence Analysis: a new ordination method to relate two community compositions. Ecology 85(3), 834--846

Author

Gavin L. Simpson.

See also

coca, plot.default

Examples

## symmetric CoCA
data(beetles)
data(plants)

## log transform the beetle data
beetles <- log(beetles + 1)

## fit the model
bp.sym <- coca(beetles ~ ., data = plants, method = "symmetric")
#> 
#> Removed some species that contained no data in: beetles, plants 

## draw a plot of the response scores
plot(bp.sym)


## plot of both
layout(matrix(1:2, ncol = 2))
plot(bp.sym, which = "response", main = "Beetles")
plot(bp.sym, which = "predictor", main = "Plants")

layout(1)