Which tool are you using, is it within Galaxy, and what tool are the inputs derived from? If you are following a Galaxy tutorial, please also share the link, and we might be able to help more.
Note that these plots when generated using CummerRbund SQLite output are problematic. Issue ticket here: https://github.com/galaxyproject/tools-devteam/issues/340
Current Galaxy tutorials: https://galaxyproject.org/learn/. Those in the upper section will work at Galaxy Main https://usegalaxy.org. Others may require the use of your own Galaxy with the appropriate configuration. Docker images exist for some tutorials, for example: http://galaxyproject.github.io/training-material/topics/introduction/
Thanks, Jen, Galaxy team