# various ways to label mds (or other ordination plots)

# default labels of site and species names
plot(fish.mds2,type='t')

# more control over what is printed
# setup the plot, but don't print anything
plot(fish.mds2,type='n')

# then add text.  
#  text requires 3 arguments (x, y, text)
text(fish.mds2$points[,1],fish.mds2$points[,2],spplist$nettype)

# alternative route, using vegan functions
mdsplot <- ordiplot(fish.mds2)
#  can also specify type = 'none', 'points', 'text' 

# use info in mdsplot object to make plots
points(mdsplot, display='species', pch=19)
#  pch changes the plot character.  see ?par for all the options

text(mdsplot, display='sites')
#  the above 3 statements will draw nMDS plot of species, label sites w/names

# something new, useful to identify sites, species, or label a few
# draw a clean plot
plot(fish.mds2, type ='n')    # or use ordiplot to create mdsplot object
identify(mdsplot, 'sites')
# use mouse to select individual points.  will be labelled
#  with site/species names, can specify new labels with 
#   label=vector of names
# identify() is also available in a non-vegan form
# identify(x, y, labels)

# draw convex hulls
plot(fish.mds2,type='n', xlab='NMDS 1', ylab='NMDS 2')
ordihull(fish.mds2,spplist$NETTYPE)

# my function to plot labels at centroids of groups
ordicentroid(fish.mds2,spplist$NETTYPE)

# for demo, plot locations of points for one group
points(fish.mds2$points[spplist$NETTYPE=='EF',])

title("Convex hulls")

# or add ellipses
plot(fish.mds2,type='n')
ordiellipse(fish.mds2,spplist$NETTYPE)
ordicentroid(fish.mds2,spplist$NETTYPE)
points(fish.mds2$points[spplist$NETTYPE=='EF',])