Plotting - Pch and rep functions in R

Question

I have completed an NMDS on biological abundances of taxa in an experiment I set up. I essentially have 3 categories that I am using in my NMDS, for simplicity sake we can just call it A, B, and C.

• A has 36 entries
• B has 35 entries
• C has 36 entries

I have no issues with the NMDS, and can get a great black and white figure that would be decent for publication. My issue is that for presentations at conferences (or for a poster) I would like to color the points to spice up the picture a bit. I am using the "rep()" function, as I am assigning symbols (and hopefully colors in the near future) to my categories.As you can see here, I can get the points solid-colored, but I think a black outline would really help make them stand out.

I have tried placing "bg=" and "col=" in places in my code that made sense, but I just cannot get a border to work. Am I missing something simple? Here is the code, and figure I have so far. NMDS plot

plot(Ulv.mds, type="n")
points(Ulv.mds$points, pch=c(rep(17, 36), rep(19, 35), rep(15, 36)),
    cex=1.1, col=c(rep("black", 36), rep("darkorange3", 35), 
    rep("purple1", 36)))

This is my first question, please let me know if you need any other information, and thanks in advance.

Answer 1

If you want to use the background bg option, you have to use pch 21 to 25. this way, you get the border you need. Int he following example, I chose colors 2:6 for the background, but you can use your formulation with rep .

plot(1:5, pch=21:25, bg=2:6, cex=2)