The number of s at the beginning of the line indicates whether it is treated as a section sub-section sub-sub-section etc. To add labels use geom_text and add the group letters from the meanyielddata dataframe you made earlier. You can enrich your comments by using Markdown syntax.
You may add a field named bibliography to the YAML metadata and set its value to the path of the BibTeX file.
Also you should have an earth-analytics directory set up on your computer with a data directory with it. R Markdown supports a reproducible workflow for dozens of static and dynamic output formats including HTML PDF MS Word. Use a productive notebook interface to weave together narrative text and code to produce elegantly formatted output. I want to slidify it so both and dont work.