plot_ordination: Plotting ordinations
In RodolfoPelinson/pelinson.et.al.2020: Data Analysis of Pelinson et al 2020

This function is to plot the ordinations from the GLLVMs.

plot_ordination(
  model_gllvm = NULL,
  LVs = NULL,
  species_loadings = NULL,
  xlim = NULL,
  ylim = NULL,
  x1,
  x2 = NULL,
  main = NULL,
  species = F,
  species_col = "black",
  name_species_col = "white",
  species_size = 4,
  sites_size = 1,
  species_names = NULL,
  sites = T,
  elipse = F,
  site_colors = NULL,
  pch = NULL,
  legend_labels = NULL,
  name_species_size = 0.8,
  legend_x = NULL,
  legend_y = NULL,
  legend = F,
  legend_horiz = F,
  legend_ncol = 1,
  ylab = "Latent Variable 2",
  xlab = "Latent Variable 1",
  alpha.elipse = 75,
  sep = F,
  plot_centroid_dist = FALSE
)

`model_gllvm`	The resultant object from function gllvm.
`LVs`	The latent variables to be plotted. If provided, the model_gllvm argument will be disregarded.
`species_loadings`	A vector containing the species ladings.
`xlim`	A vector of length = 2 with upper and lower limits of the x axis
`x1`	First grouping variable
`x2`	Second grouping variable
`main`	Main Title
`species`	Should species be plotted?
`species_col`	Species colors. Either a color or a vector of colors with length equal to the number of species.
`species_size`	Species sizes Either a color or a vector of colors with length equal to the number of sites.
`sites_size`	Sites sizes. Either a number or a vector of numbers with length equal to the number of sites.
`species_names`	Species names to be plotted. A vector of the names of the species.
`sites`	Should sites be plotted?
`elipse`	Should ellipses around treatments be plotted?
`site_colors`	Sites colors. Either a color or a vector of colors with length equal to the number of sites.
`pch`	Tipe of dots to plotted for sites.
`legend_labels`	Labels for the legend.
`name_species_size`	A cex value for species names. Either a number or a vector of numbers.
`legend_x`	x coordinates to plot the legend
`legend_y`	x coordinates to plot the legend
`legend`	Should legend be plotted? Default to F.
`legend_horiz`	Should legend be horizontal?
`legend_ncol`	Number of columns in the legend.
`ylab`	Label of y axis.
`xlab`	Label of x axis.
`alpha.elipse`	Transparency for the ellipses.
`sep`	Should plots be separated by isolation distance to improve visualization?
`plot_centroid_dist`	Should distances between centroids within distances be plotted?
`ylimy`	A vector of length = 2 with upper and lower limits of the x axis