How to avoid overplotting (for points) using base-graph?

Question

I am in my way of finishing the graphs for a paper and decided (after a discussion on stats.stackoverflow), in order to transmit as much information as possible, to create the following graph that present both in the foreground the means and in the background the raw data:

However, one problem remains and that is overplotting. For example, the marked point looks like it reflects one data point, but in fact 5 data points exists with the same value at that place.
Therefore, I would like to know if there is a way to deal with overplotting in base graph using points as the function.
It would be ideal if e.g., the respective points get darker, or thicker or,...

Manually doing it is not an option (too many graphs and points like this). Furthermore, ggplot2 is also not what I want to learn to deal with this single problem (one reason is that I tend to like dual-axes what is not supprted in ggplot2).

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Update: I wrote a function which automatically creates the above graphs and avoids overplotting by adding vertical or horizontal jitter (or both): check it out!

This function is now available as raw.means.plot and raw.means.plot2 in the plotrix package (on CRAN).

Answer 1

Standard approach is to add some noise to the data before plotting. R has a function jitter() which does exactly that. You could use it to add the necessary noise to the coordinates in your plot. eg:

X <- rep(1:10,10)
Z <- as.factor(sample(letters[1:10],100,replace=T))

plot(jitter(as.numeric(Z),factor=0.2),X,xaxt="n")
axis(1,at=1:10,labels=levels(Z))