1) This has nothing to do with bioinformatics (try an R forum), so I'll close the post. 2) You R code wouldn't even work, since the bottom axis is 1, not 0, and you meant xaxt rather than xant.

Edit: I'll add that the trick is something like:

x <- seq(10,200,10)
y <- runif(x)-0.5
d <- data.frame(x=x,y=y)
g <- ggplot(d, aes(x=x,y=y))
g <- g + geom_point()
g <- g + theme_bw()
g <- g + theme(panel.grid=element_blank(), panel.border=element_blank(), axis.line=element_line(), axis.line.x=element_blank())
g <- g + geom_abline(intercept=0, slope=0)
g

Edit2: See also this issue report.