Transparency with polygon command

You can use The function rgb() to specify a color with an alpha transparency.

for example :

xx <- c(1:50)
 yy <- rnorm(50)
 n <- 50
 hline <- 0
plot (yy ~ xx, type="n", axes=FALSE, ann=FALSE)
text(x=xx,y=min(yy)+max(yy),labels='a')
polygon(c(xx[1], xx, xx[n]), c(min(yy), yy, min(yy)),    
        col=rgb(1, 0, 0,0.5), border=NA)

Another convenient possibility for making a lighter/more-transparent version of an existing color is to use adjustcolor(), something like

adjustcolor("red", alpha.f=0.5)