Update: Better labels on graphs added.
Edit: just realized that my graphs are poorly titled. They are graphing the percent methylation at DMR sites. Will update them as soon as I can.
Worked on graphing Day 10 DMRs by treatment. I first tried a plot with means by treatment for all DMRs in a single plot but that was difficult to read, so I settled on individual box plots by location as I felt this captured both the location as well as the variation in the data.
A few example plots:
Code, and a walkthrough of the process is available here
A PDF of the plots can be downloaded here