title: How to avoid overplotting (for points) using base-graph?
body: <p>I am in my way of finishing the graphs for a paper and decided (<a href="https://stats.stackexchange.com/questions/2067/follow-up-in-a-mixed-within-between-anova-plot-estimated-ses-or-actual-ses">after a discussion on stats.stackoverflow</a>), 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:
  <img src="https://i.stack.imgur.com/mLNqy.png" alt="alt text"></p>
  
  <p>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.<br>
  <strong>Therefore, I would like to know if there is a way to deal with overplotting in <code>base graph</code> using <code>points</code> as the function.</strong><br>
  It would be ideal if e.g., the respective points get darker, or thicker or,...  </p>
  
  <p>Manually doing it is not an option (too many graphs and points like this). Furthermore, <code>ggplot2</code> 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 <code>ggplot2</code>).</p>
  
  <hr>
  
  <p><strong>Update:</strong> I wrote a function which automatically creates the above graphs and avoids overplotting by adding vertical or horizontal jitter (or both): <a href="http://www.psychologie.uni-freiburg.de/Members/singmann/R/raw.means.plot" rel="nofollow noreferrer">check it out!</a></p>
  
  <p>This function is now available as <code>raw.means.plot</code> and <code>raw.means.plot2</code> in the <a href="http://cran.r-project.org/web/packages/plotrix/index.html" rel="nofollow noreferrer"><code>plotrix</code></a> package (on CRAN).</p>