I have uploaded a draft of Chapter 3 — Plotting Fundamentals — for the Introduction to Fisheries Analyses with R (IFAR) book (note the new name).  This chapter is meant to be a quick introduction to plotting in base R for plots typically constructed by fisheries scientists (histograms, scatterplots, line plots, plots with intervals (e.g., confidence), etc.).  There is also a brief introduction to setting plotting parameters, plotting multiple plots relative to each other (e.g., side-by-side), and output formats.