Alter axes in R with NMDS plot

Question

I'm trying to change the axes in my NMDS plot to zoom into where my sites are plotted. I assume that the space chosen in a product of the species points which I do not have plotted. I have tried adding xlim to my code to no avail and was wondering if I have it in the wrong place or if another action is needed. Below is a copy of my code.

#NMDS on pooled abundance with NA's omitted
NMDS_HPA<-metaMDS(HP_Abundance_omit[,-1],k=2, trymax=1000)
plot(NMDS_HPA, type="n", display="sites", xlim=c(-1.5,1.5))
with(descriptors, levels(T)) 
colorvec<-c("seagreen4", "tan4", "mediumblue")
plot(NMDS_HPA, type="n", xlim=c(-1.5,1.5))
title(main="NMDS using Abundance with Bray-Curtis", sub="Habitats Pooled")
ordihull(NMDS_HPA, groups=treat, draw="polygon", col="grey90", label=F)
with(descriptors, points(NMDS_HPA, display="sites", col=colorvec[T], pch=21, bg=colorvec[T]))
with(descriptors, legend("topright", legend=levels(T), bty="n", col=colorvec, pch=21, pt.bg=colorvec))

Thanks

Answer 1

If you don't set the ylim too, then vegan has no choice but to show more (or less) of the x-axis than you want because the scaling of the axis must be retained; a unit change along one axis must match the same unit change along the other. Otherwise, how would you know how to represent Euclidean distances (easily) on the figure? As those Euclidean distances are supposed to reflect the rank ordering of the original dissimilarities, maintaining the aspect ratio or relative scaling of the axes to one another is important.

You can see this in action just by using your mouse to rescale the size of the device window on screen. R replots the figure using different axis limits all the time in order to maintain an aspect ratio of 1.

Consider this reproducible example:

library("vegan")
data(dune)

set.seed(56)
sol <- metaMDS(dune)

Choosing a section in both the x and y axes works as expected

## zoom in on the section (-0.5,0.5)(-0.5,0.5)
plot(sol, xlim = c(-0.5, 0.5), ylim = c(-0.5,0.5))

If you want to retain the full y-axis but only show say the middle 50% of the x axis then you have to plot on a device whose width is ~ 50% that of the height (approximately because R's default is to use different sized margins on the top/bottom left/right margins.)

png("~/mds-zoom2.png", height = 700, width = 350, res = 100, pointsize = 16)
plot(sol, xlim = c(-0.5, 0.5))
dev.off()

which produces

This is almost right. You could solve the problem exactly by setting the margins equal around the plot using par(mar = rep(4, 4) + 0.1) and then work out the ratio of the range of the scores on the x and y axes (get the scores(sol) and compute the range() on both columns then compute the ratio of the two ranges), then use that to give you the desired height of the plot for the width you want to state.