I usually prepare diagrams and plots using my statistical software (like R) and process the resulting .emf (enhanced metafile) via Inkscape, which is vector based and offers very good tools for graphic manipulation.
For figures and photos I also like using GIMP, which is basically a free Photoshop.
Both softwares are completely free and available for GNU/Linux, OS X, Windows and more operating systems. There are also good tutorials for getting familiar with them.
https://inkscape.org/
https://www.gimp.org/
You can take a look into what is best fitting your requirements. I hope you find what you are looking for :)