Hi again, @ptalebic!
Many QIIME 2 visualizations have “Download as…” buttons when opened in q2View.
These can be edited in whatever image editor you like. Pulling down an SVG of the alpha-diversity plot, it’s easy to open it with inkscape or similar, and then colorize as needed. The paint-bucket tool works like a charm for coloring box plots.
I don’t believe a similar feature is available for alpha-rarefaction, but it’s worth checking. In a pinch, you do have other options. It’s always possible to take a screen capture and edit that as needed (though raster files like .png are often less flexible for this kind of work). It’s also possible to export the raw data (see the exporting tutorial), and visualize with whatever tool you prefer. (python, R, excel, whatever makes you smile.)
Hope this helps,