I have seen examples of graphs embedded very "natively" in papers:
The snippet shown is taken from here. It is not a particularly beautiful diagram or anything but what's nice about it is that these graphs are very natively embedded in the LaTeX PDF. For instance, I can select the text of the X and Y axis labels and all the text labels in the middle. I have seen experienced researchers do this and I would like to know how.
Here's what I have tried:
Created similar graphs in R and Python and then tried to port the resulting EPS image into LaTeX. It doesn't look bad, however, that is not as native (one can't select the text within the image as I mentioned above). It is hard to explain but when I do this the image is one intact object and nothing inside it can selected in PDF. However, in the image shown above, the graph seems to be more "modular"(?) such that you can select different text labels in it.
I am aware of the tikz package in LaTeX, however, I doubt that these researchers are manually typing in coordinates of the graph details into a tikz image. So maybe some software is being used to convert an R image into a native tikz image?

tikzandpgfplotswithout manually typing coordinates. – May 09 '20 at 22:51stack plots=yin the pgfplots manual. The left one can can e.g. done with two node chains of some nodes that you could design withpath picture, and some loop for the connections. Everything is rather straightforward if you have the data in a structured way. – May 09 '20 at 23:00Rthat will export your graph into atikzpicture? I'd rather not "program" in LaTeX and let a package inRorpythondo the translation for me. – learnerX May 09 '20 at 23:12matplotliband save as PDF, the text in that figure is selectable when included in a document with\includegraphics. – Torbjørn T. May 10 '20 at 07:33