To answer your questions:
- What does the appended '2' do to the color? Does that work for any color?
There are a bunch of named colors that you can access in R (for example, see page 3 of this document). Many of these colors come in multiple shades, with names like "yellow1", "yellow2", etc., with higher numbers generally representing darker shades of the given color. If you type colors(), R will output a vector of all the color names. If you want to view some of these colors quickly, you can do, for example, library(scales); show_col(colors()[grep("yellow", colors())]).
2)If I understand your explanation, the "stroke=0 " should remove the marker outlines, but mine still has them. Did I miss something?
stroke sets the border thickness. I'm not sure why stroke=0 isn't working for you. However, you can also try:
geom_point(aes(fill=factor(flag)), size=4, shape=21, stroke=NA) +
or
geom_point(aes(fill=factor(flag)), size=4, shape=21, color="#00000000") +
The last two zeros in color="#00000000" make the color transparent, equivalent to alpha=0.