plot.cord {ecoCopula}

Plots an ordination of latent variables and their corresponding coefficients (biplot).

Description

Plots an ordination of latent variables and their corresponding coefficients (biplot).

Usage

## S3 method for class 'cord'
plot(
  x,
  biplot = FALSE,
  site.col = "black",
  sp.col = "blue",
  alpha = 0.7,
  arrow = TRUE,
  site.text = FALSE,
  labels = dimnames(x$obj$fitted),
  ...
)

Arguments

x

is a cord object, e.g. from output of cord

biplot

TRUE if both latent variables and their coefficients are plotted, FALSE if only latent variables

site.col

site number colour (default is black), vector of length equal to the number of sites

sp.col

species name colour (default is blue), vector of length equal to the number of sites (if arrow=TRUE)

alpha

scaling factor for ratio of scores to loadings (default is 0.7)

arrow

should arrows be plotted for species loadings (default is TRUE)

site.text

should sites be labeled by row names of data (default is FALSE, points are drawn)

labels

the labels for sites and species (for biplots only) (default is data labels)

...

other parameters to be passed through to plotting functions.

Value

an ordination plot.

Examples

X <- spider$x
abund <- spider$abund
spider_mod <- stackedsdm(abund,~1, data = X, ncores=2) 
spid_lv=cord(spider_mod)
#colour sites according to second column of x (bare sand)
cols=ifelse(spider$x[,2]>0,"black","red")
plot(spid_lv,biplot = FALSE,site.col=cols, site.text = TRUE)


library(ggplot2)
library(RColorBrewer)
alpha= 2.5
site_res <- data.frame(spid_lv$scores,X)
sp_res <- data.frame(spid_lv$loadings,species=colnames(abund))
ggplot()+
 geom_point(aes(x=Factor1,y=Factor2,color = reflection ),site_res)+
 geom_text(aes(x = Factor1*alpha, y = Factor2*alpha,label = species),data=sp_res)+
 scale_color_gradientn(colours = brewer.pal(n = 10, name = "PuOr"))+
 theme_classic()