I am using a similar plot code below, I am trying to compile in the same plot multiple traits, but not sure how can I save the plot afterwards.
par(mar=c(5.1, 4.1, 1.1, 1.1))
ymx <- maxlod(out_bin)
plot(out_bin, map, lodcolumn=1, col="slateblue", ylim=c(0, ymx*1.02))
plot(out_bin, map, lodcolumn=2, col="violetred", add=TRUE)
legend("topleft", lwd=2, col=c("slateblue", "violetred"), colnames(out_bin), bg="gray90")