Tell me how wrong I am for using TikZ. I bloody love stuff like TikZ in LaTeX or PIL in Python for making 2D stuff. GUIs hurt my feelings. 
I think tikz might not be for you. Does R offer a library based on cairo?
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More here in why tikz is likely not suitable for what you mentioned https://tex.stackexchange.com/questions/51757/how-can-i-use-tikz-to-make-standalone-svg-graphics …
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You can add most latex packages to RMarkdown files and write equations in latex. I'll have a play with TikZ and see if it's the same.
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Ah, FWIW I make all my tikz images in as plain latex as possible and then move them to my fancy beamer class.
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Eventually they need to be saved as separate PDFs of course if included in a manuscript.
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