blog/2025/visible-pca/

[giscus[bot]]

blog/2025/visible-pca/

This blog post delves into the my personal Long Covid data, collected via the Visible app, using Principal Component Analysis (PCA). I detail four key clusters: Menstruation, Exertion, Emotional, and Neurological and then compare these clusters to the principal components derived from PCA. The analysis aims to provide a validated, data-driven framework for exploring my symptoms during this condition, using clear visualisations to showcase the results.

https://drmowinckels.io/blog/2025/visible-pca/

[fjodor]

Great post! First of all, wishing you good recovery to full health.
I liked how you kept digging deeper and how you connected clustering and PCA. Well done.
Some nice coding tricks in there! Great use of purrr and custom functions.
You may want to look into tidytext::reorder_within() to order categories within facets. Combine with scale_x_reordered() or scale_y_reordered().
geom_col() short for geom_bar(stat = "identity").
Are you using a custom theme with viridis colors as default?

[drmowinckels]

Thanks for reading and commenting!

I've never actually used tidytext, so I'll check out that functionality. Sounds like a nice way to work just with ggplot rather than list columns (though I'm quite comfortable doing that).

You know, I keep forgetting geom_col is a thing!

Yes, I've set custom options for my website repo so that all the ggplot images get the same look.

options(
  ggplot2.discrete.colour = scale_colour_viridis_d,
  ggplot2.discrete.fill = scale_fill_viridis_d,
  ggplot2.continuous.colour = scale_colour_viridis_c,
  ggplot2.continuous.fill = scale_fill_viridis_c
)

[fjodor]

Thanks for answering! Nice settings.

[KNBaldwin]

Wow! This is incredible. I just got the Visible armband yesterday and cannot wait to see where improvements can made. I'll admit I only made it through a small portion of your writing. I'm an attorney and although I am trained to read and comprehend dense and complex data, I am not able to do that now.

If you had just had 3-5 most important take aways from your article, what would they be?

Interestingly, i'm in a crash and have such severe shortness of breath so I found what you saud about hypoxia very interesting.

Although nobody wants to be this ill, this community is thankful that you're here and hopefully, you will get substantially better and can update us on the science and data behind recovering. We also hope you will scream from the rooftop to your colleagues in science that we are desperate. Post viral illness from EBV hit an all time high back in the 80s. Over 40 years ago.

Imagine those who have struggle for 40 years or more. So, please get better. We need you in this community to help break down the science and data and be a voice to other researchers that this illness needs attention badly.

Best wishes!

[drmowinckels]

I'm happy to hear you are taking steps to get better! I really hope the armband gives you a good tool to working with in your won recovery!

My wife actually has ME/CFS, and has had for over 15 years, so I know how horrible this can be in the long run. Getting long covid (or post viral fatigue) was on the top of our worst-case scenarios from the pandemic. Which is why I managed to avoid getting COVID at all for 4 years. And then was unlucky enough to have this happen.