What approach do you use for 3d plotting in Rmd (notebooks and documents)

Sometimes, 3d plots help. They can be complex/risk obscuring information, but still valuable when trying to understand information across multiple dimensions.

What techniques/ tools to you use to approach embedding these visualisations in R markdown outputs? I've played with plotly, though I'm unsatisfied with the programmatic interface (just personal opinion, I dislike the idioms), and also with rgl, though I've been having trouble getting it to render in outputs (despite playing with knit_hooks$set(webgl = hook_webgl), etc).

Are there any other solutions that people recommend?

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I've had some success with Plotly, but only tried it once. Results were visually pleasing, and the saved HTML worked flawlessly in the browsers I tried. Like you, I wasn't too excited about the programmatic interface, and the documentation was not always as helpful as I had hoped.

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Another option is rthreejs. I haven't tried it but the examples look very nice.