Proper use of scaling on axes from ordinations (like MDS and PCA)?

Moving a conversation from slack over to discourse because there’s a bunch of useful stuff that I’d like preserved, but also because we haven’t actually reached a consensus answer.

The original question (by me):

Question about ordinations (came up in When plotting an ordination from multidimensional scaling (PCoA), is it important to keep the axes on the same scale? Eg. if the first axis is -1 to 1, and the second is -0.5 to 0.5, should the distance between the farthest points in the first dimension be twice that in the second dimension?

I thought that the units of the axes were arbitrary (since distance need not be metric) so the scaling doesn’t actually matter, but Michael seems to think differently. Also, is it the same or different when doing PCA or other ordinations?

I’ll let @mkborregaard lay out his current position and respond as needed, but other perspectives would be welcomed.

Yes, I think aspect ratio should be equal, because the units of x and y are the same. I think it gives the most fair image, also of the degree of variation on each axis.
I also believe it is the convention - on Slack I came with a number of references to the use of equal aspect ratio:

This blog post from one of the developers of R’s vegan package (the R package for community ecology) recommends customising ordination plots by setting aspect ratio to 1:

So does the owner of the ggvegan package, R’s package for making ordination plots with ggplot2:

So does the asker of this SO question:

Here’s a paper that argues for a different method - scaling pca plots by the eigenvalues on the axes. That must be considered an alternative method. They even write how the peer reviewers remarked on the aspect ratio not being equal

For MDS, which is distance-preserving, I would also argue that distances are best preserved with aspect ratio 1. I laid out this argument and small toy analysis for it:

When you plot the points, it translates the x and y values into pixel positions on the screen. this is equivalent to multiplying x with a constant a that depends on the pixel concentration, the extent of the x axis in screen pixels and the values associated with the x axis limits, and multiplying y with b that depends on the same attributes of the y axis
The aspect ratio is then defined as c = a/b, so given that all of these are constant the plot coordinates are proportional to multiplying y with c.

Now if we take an example

using StatsPlots, Distances, MultivariateStats
m = rand(100, 10)
dm = pairwise(BrayCurtis(), m)
mds = fit(MDS, dm, distances=true)
proj = projection(mds)
x, y = (proj[:,i] for i in 1:2)

We’ve fit a PCoA to the dm distance matrix of distances among m, and extracted the first two components, x and y, which is the translation into two dimensions that best maintains the distances between points. Now let’s calculate the correlation between the distances on the plot and the distances among the input points. To do that we need to multiply by the aspect ratio, c.

using Statistics
function getcor(c, dm, x, y)
       fin = pairwise(Euclidean(), vcat(x', c .* y'), dims = 2)
       cor(vec(fin), vec(dm))
 res = [getcor(i, dm, x, y) for i in 0.1:0.01:3]
 plot(0.1:0.01:3, res)

Here’s the result

1 looks like a good aspect ratio here. It would be cool to see this for a real-life code case with non-Euclidean distances, as that is what MDS is often used for.

Here’s a real-life example (human microbiomes) trying out your code. I calculated the pairwise Bray Curtis dissimilarity and plotted it as you suggested:

So here the peak is closer to c ≈ 0.6. I’m guessing that the discrepancy is because, in a random matrix, there probably aren’t axes that describe a disproportionate amount of the variation. Looking at a scree plot, for my data:

Compared to one for a random matrix with the same number of dimensions:

I find this genuinely interesting, as I was expecting the pcoa to maintain distances. I wonder - could this be related to the eigenvalue ratio, as suggested in the F1000 paper? And does anyone else here know anything about this? :slight_smile:

I wonder - could this be related to the eigenvalue ratio, as suggested in the F1000 paper?

If it is, it’s not straightforward. Using my real life example, I took some subsets of the data and calculated the aspect ratio with the highest correlation (maxc), what that correlation was (maxcor) and the ratio of eigenvalues. Here’s what I found:

function maxcor(mds, dm; dim1=1, dim2=2, rng = 0.1:0.01:3)
    proj = projection(mds)
    x, y = (proj[:,i] for i in [dim1, dim2])

    e1, e2 = eigvals(mds)[[dim1, dim2]]
    res = [getcor(i, dm, x, y) for i in rng]
    (mc, i) = findmax(res)
    return (maxc = rng[i], maxcor=mc, eigratio=e2/e1)

function ploteigs(dm; dims=50, points=200)
    c = Float64[]
    er = Float64[]
    cor = Float64[]
    for _ in 1:points
        picks = rand(1:size(dm, 1), dims)
        subdm = dm[picks, picks]
        mds = fit(MDS, subdm, distances=true)

        for i in 1:5
            mc = maxcor(mds, subdm, dim1=1, dim2=i)
            push!(c, mc[:maxc])
            push!(er, mc[:eigratio])
            push!(cor, mc[:maxcor])
    scatter(c, er, zcolor=cor)


Just for funsies, here it is with a random matrix:

You should set aspect_ratio = 1 in those plots, given that the scales of x and y are supposed to be the same :smiley:


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What’s going on with all those where the eigenvalue ratio is 1?

No idea… we really need someone that knows what they’re talking about to join this conversation :stuck_out_tongue:

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BTW I think it’s a bug that Plots adjusts the image size by the aspect_ratio. It should use aspect_ratio to redefine the x and y lims