Wayne's Bioinformatics Code Portal fomightez

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.

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

	import pandas as pd
	import numpy as np
	import matplotlib as mpl
	import re

	df = pd.DataFrame({
	"Gene_name": ["sdsR", "arrS","gadF"],
	"Genes_in_same_transcription_unit": ['pphA, sdsR', 'arrS','mdtF, mdtE, gadF, gadE'],
	})
	# Convert Gene_name column to a set for quick lookup