I'm using these tutorials as a place to keep track of code I've used to generate R visualizations and statistical analyses, specifically for the purpose of visualizing and analyzing large microbial ecology datasets. I also talk about the analyses/visualizations here in terms of microbial amplicon/marker gene data, but these analyses can be extended for use in nearly any situation with a sample x species abundance/frequency, or sample x numerical variable type output. There are probably hundreds of different ways to obtain the same end product in R, so feel free to adapt things as needed.
There are some really great statistics resources out there. My go to is GUSTAME, which is a guide to statistical analysis in microbial ecology. Also their papers: