Do you know how to plot this figure? I found many of them in Nature journals but have not figured out how to make them. Which software/tool do you suggest? Thank you very much.
I'm not exactly an expert, but I believe both images were made in PowerPoint. You'd be amazed at what you can achieve if you take the time and learn the ropes.
As Valerio Pampanoni mentions, these could be replicated in PowerPoint - if one has beyond expert level PowerPoint skills and very experienced with the dark corners of the PowerPoint interface. I have 30+ years experience with all sorts of graphic arts software and CAD, so although I could do it, and have at times done similar art, but only with a gun held to my head.
This isn't a negative on PowerPoint, it simply wasn't intended for this complexity. It would be far easier, even without much experience, to use a tool like Adobe Illustrator or the free Open Source application Inkscape ( https://inkscape.org/ ) - and that skill would be a very useful as you move forward in your career.
The big drawbacks coming immediately to mind are that PowerPoint has no 'Layers', so you can't lock or hide what you don't want selected as you work, PowerPoint has very weak ability to make and apply styles, very limited drawing tools, and the fatal flaw, if you intend on professionally publishing is it is wretched at importing external assets and exporting in pre-press quality formats (font handling, masking like those images inside of hexagons, etc.) for instance). I use Illustrator and Inkscape pretty much interchangeably.