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what do you use to make figures? Like a visual representation of a part of your work (i.e., arrow here, arrow there linking words/equations) that you want to include in your paper?
Also, typically, do you attach your figures/tables separately when submitting your paper, and the editors of the journal will find a way of incorporating it in the paper?
I use Prism to create the base figure, then edit it in Powerpoint. Additionally, some people use Adobe Illustrator or Photoshop to alter the figures (arrows, etc.)
To answer how to incorporate figures/tables, that is specific to the journal you submit it to. They will tell you in the "Author Guidelines" for each journal. Typically they are separate files that get incorporated later, but again not always.