How to center boxes on top of lines in the legend of a plot?

Question

I would like to superimpose transparent boxes on top of the lines in the legend.

A small example:

xdata <- 1:7
y1 <- c(1,4,9,16,25,36,49)
y2 <- c(1, 5, 12, 21, 34, 51, 72)
y3 <- c(1, 6, 14, 28, 47, 73, 106 )
y4 <- c(1, 7, 17, 35, 60, 95, 140 )

plot(xdata, y1, type = 'l', col = "red")
lines(xdata, y2, type = 'l', col = "red", lty = 3)
lines(xdata, y3, type = 'l', col = "blue") 
lines(xdata, y4, type = 'l', col = "blue",  lty = 3)

# add legend with lines
legend("topleft", legend = c("Plot 1", "Plot 2", "Plot 3", "Plot 4"),
      lty = c(1,3,1,3), lwd = rep(1.3 ,4),
      col = c("blue", "blue", "red", "red") ,
      pch = rep(NA, 4), cex = 0.8, 
      x.intersp = 0.7, y.intersp = 1.2, bty = 'n')

# add boxes
legend("topleft", legend = c("", "", "", ""), lty = rep(0, 4), 
       col = c(adjustcolor(blues9[3], alpha.f = 0.6), 
               adjustcolor(blues9[3], alpha.f = 0.6), 
               adjustcolor("red", alpha.f = 0.1), 
               adjustcolor("red", alpha.f = 0.1)),
        pch = rep(15, 4), cex = 0.8, pt.cex = rep(2, 4),
        x.intersp = 0.7, y.intersp = 1.2, bty = 'n')

which produces:

As you can see, the boxes are shifted to the left along the lines in the legend.

How can I set the alignment of the boxes, so that they become horizontally centered on top of the line symbols in the legend? Thanks!

Answer 1

The clue here is to specify the same lwd in both legend calls, i.e. also in the call for the boxes where lty = 0.

Here's a simpler example, with only the arguments relevant for your actual issue:

plot(1)

# lines
legend(x = "topleft",
       legend = c("Plot 1", "Plot 2", "Plot 3", "Plot 4"), bty = 'n',
       lty = c(1, 3), lwd = 1,
       pch = NA,
       col = rep(c("blue", "red"), each = 2))

# boxes
legend(x = "topleft", 
       legend = rep("", 4), bty = "n",
       lty = 0, lwd = 1, # <- lwd = 1  
       pch = 15, pt.cex = 2,
       col = c(rep(adjustcolor(blues9[3], alpha.f = 0.6), 2),
               rep(adjustcolor("red", alpha.f = 0.1), 2)))

---

If you're fine with a coloured outline of the boxes, one legend call is enough. Just use a pch which accepts pt.bg (here: 22):

plot(1)
legend(x = "topleft",
       legend = c("Plot 1", "Plot 2", "Plot 3", "Plot 4"), bty = 'n',
       lty = c(1, 3), col = rep(c("blue", "red"), each = 2),
       pch = 22, pt.cex = 2, 
       pt.bg = c(rep(adjustcolor(blues9[3], alpha.f = 0.6), 2),
                 rep(adjustcolor("red", alpha.f = 0.1), 2)))