NMDS Ellipse Interpretation

[camrynbigelow]

Hello,

I am having trouble specifically interpretating what the ellipses mean in the NMDS. I used the hidden function provided, but I am unsure if the ellipse was plotted with standard error or standard deviation using this script. Could you provide any clarification, please?

Sincerely,

Camryn

[trippster08]

Hi Camryn,
I am so sorry, that section was not supposed to be there. I was having difficulties getting it to work, and meant to delete this part:

I want
define hidden vegan function that finds coordinates for drawing a covariance ellipse
veganCovEllipse <- function(cov, center = c(0, 0), scale = 1, npoints = 100) {
theta <- (0:npoints) * 2 * pi / npoints
Circle <- cbind(cos(theta), sin(theta))
t(center + scale * t(Circle %*% chol(cov)))
}

Once I got it to work, then I was going to evaluate and describe what it does, but I haven't gotten to most of the description yet, since I've been focusing mostly on the hydra analysis version, since that is what most of the people here are using (sorry). I'm actually starting to revise this pipeline to simplify it and to make it work with any number of genes, as long as the primer files exist and are in the correct format, but that is just getting started.

I'm sorry about the confusion.

[trippster08]

To see how it was used correctly, see the page Vegan Tutorial. There is also a link to it in the README file. Between this page and the Vegan package page, there are a lot of cool things that can be done to visualize your data. This pipeline just has a few simple ones, mostly as examples. This visualization section was developed for our metabarcoding workshop, so I decided to add it here to make it more public, since I took the time to write it.

[camrynbigelow]

Thank you for clarifying. I have seen others use the function in a similar manner and that standard deviation or standard error were used. It seems to work, but I would like to be able to explain what exactly it is, so I will use a different visualizing step from vegan.

…

On Mon, Jul 21, 2025 at 9:05 AM Tripp Macdonald ***@***.***> wrote: *trippster08* left a comment (trippster08/Metabarcoding_on_RStudio#4) <#4 (comment)> To see how it was used correctly, see the page Vegan Tutorial <https://peat-clark.github.io/BIO381/veganTutorial.html>. There is also a link to it in the README file. Between this page and the Vegan <https://vegandevs.r-universe.dev/vegan> package page, there are a lot of cool things that can be done to visualize your data. This pipeline just has a few simple ones, mostly as examples. This visualization section was developed for our metabarcoding workshop, so I decided to add it here to make it more public, since I took the time to write it. — Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BC24Z6NHFX456TD7K7AKHJD3JTXQ3AVCNFSM6AAAAACB5CTGSGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTAOJWHEZDAMZZHA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- *Camryn Bigelow (she/her/hers)* Graduate Research Assistant | Piller Lab Department of Biological Sciences Southeastern Louisiana University Hammond, Louisiana 70402