What kind of 2D plot or matrix to use for distance and similarity indices?

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Alessandro Giuliani

You can order your distance matrix in this way so to put in light clusters:

https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bti329

Edgar Guevara

Maybe a bubble plot might be useful, such as Hans Rosling's (RIP)

https://www.gapminder.org/tools/#_locale_id=en;&chart-type=bubbles