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At this time, this isn't an answer as such, but rounds out more of what the original poster should have included.
Plus, this reply points out that the issue doesn't seem to really interfere with observing what the plot is meant to illustrate.

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Replicating the issue and getting the full error traceback that should have been included in the post

Searching 'Replicate Andrew's example on PCA' in Google, lead me to the notebook here, which looks to be the same as the OP is running.

I then obtained that notebook and uploaded it to a fresh remote session (served by the MyBinder service) started from the launch badge here. (Or you can just [click here](https://mybinder.org/v2/gh/fomightez/cluster_analysis

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The demonstration notebook , related to SO question 'How to export all output from certain Jupyter cell, say, using %%capture magic, and save output to a PDF file?', was developed and works in MyBinder-served Jupyter sessions launched from here. However, the easiest way to launch is to click here so this demo notebook will be opened in that environment. (It was set up to have the PDF making step work with `!jupyter nbconvert --no-input -

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# Demonstrating "you can now uv run scripts (with inline deps!) from stdin and URL" https://x.com/trevmanz/status/1846301009053970542 and trying
# with the gist use suggestion in https://x.com/trevmanz/status/1846301011809558877
# How to: go https://github.com/fomightez/3Dscatter_plot_mod_playground-binder and launch a session. Install `uv` via `pip install uv`, then run `uv run https://gist.githubusercontent.com/fomightez/3d90c4e5594ddcdf6dd023a80959c107/raw/8b940f9fe9b5a2c0ccc20635cbbd0cce7ef01b53/gist_test.py`
# /// script
# requires-python = ">=3.12"
# dependencies = [
#     "rich>=13.9.2",
# ]
# ///

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