What's the R version of example plot code?

[baif666]

I modified your example plot code and try it, but I found it plot one point twice (into 2 points), I guess this is the problem of plot() or points() function. What's the R version of this example plot code?
plot(mod$u, pch = 19, cex = 2, col = "grey90", xlab = "Factor 1", ylab = "Factor 2")
points(mod$u[meta$Group.ID == "Russia_Yamnaya",], pch = 8, cex = .6, col = "darkblue")
points(mod$u[meta$Group.ID == "Anatolia_N",], pch = 8, cex = .6, col = "salmon3")
My R version is:
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 3
minor 5.1
year 2018
month 07
day 02
svn rev 74947
language R
version.string R version 3.5.1 (2018-07-02)
nickname Feather Spray
I changed it into this way and it worked
plot(f4_mod$u[,1], f4_mod[,2], pch = 19, cex = .5, col = "grey90", xlab = "Factor 1", ylab = "Factor 2")
points(f4_mod$u[meta$V4 == "XXXX",1], f4_mod[meta$V4 == "XXXX",2], pch = 8, cex = .3, col = "yellow3")