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))
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.