rstatisticsveganmds

NMDS display and point symbol questions (vegan in r)


I've successfully produced NMDS plots (monoMDS, bray-curtis, 3 dimensions, local model). Each point represents an animal and their diet composition.

I have two questions:

(1) how do I change the symbology of points to show 2 levels (a or j) within 1 column (Life stage) on the NMDS plot?!

(2) How should I show 3D NMDS, I can't get the 3D orgl- functions to work on the 3D plot. Should I just make a few plots showing different dimensions in 2D? Looking for thoughtful ideas.

The code used:

    plot((BC.NMDS.length.corr), choices = c(1, 2), type = "points",
          xlim = c(-2.0, 2.0),las = 1, ylim = c(-1, 1), 
          xlab = "NMDS Axis 1", ylab = "NMDS Axis 2",mgp = c(3.25, 1, 0), 
          cex.lab = 1.35, cex.axis = 1.25)

    with(DATA, 
         points(BC.NMDS.length.corr, Class, draw = "points",col = "gray0", 
                show.groups = "Adult",label = TRUE, lty = 1, lwd = 2))

Solution

  • Using an example of what you want with the default example of the package:

         # Load library
           library(vegan)
         # Load data
           data(dune)
         # Compute the distance
           dis <- vegdist(dune)
    

    Specify if you want a 3D plot, the representation of the three dimensions

         # Run monoMDS
           m <- monoMDS(dis, model = "loc", k=3)
    
         # The 3D representation
           plot(m)
         # Load library for 3D representation
           library(scatterplot3d)
    

    Coordinates are in m$points; each column referring to each dimension.

         # Graphical representation
           scatterplot3d(x=m$points[,1], y=m$points[,2], z=m$points[,3])
    

    Additionally, if you want to colour the plots depending on a factor, you can specify color=A, where A is a numeric value where groups are codified.