Specific comments (Point deductions in parenthesis at the end of comments when applicable):
Your plots could benefit from a more informative legend title (or lack of!)
The stacked histograms are hard to read, especially at 30x. The geom_line() over the simulated data would have sufficed. (-0.1 per plot)
Any particular reason you used R-markdown instead of an Rscript? I don’t see any knit HTMLs, and the PNGs seem to be output using ggsave() anyways.
Next time please include your intermediate files (e.g.: genome_coverage.txt) so I don’t have to compile your code. How did you handle input files for different plots with the same file name?
Try to push more often, with more informative comments on each commit.
Specific comments (Point deductions in parenthesis at the end of comments when applicable):
Otherwise great work!
Code: 5/5 Answers: 3/3 Plots: 1.7/2
Total: 9.7/10