plot.cord: Plots an ordination of latent variables and their...

In ecoCopula: Graphical Modelling and Ordination using Copulas

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()

ecoCopula documentation built on March 18, 2022, 6:56 p.m.