title: is ggplot2 facet_grid producing an extra category?
body: <p>I tried googling and searching through forums to see if someone had the same issue, but I couldn't find anyone with a problem like this one. It's possible that it is because I am overlooking something completely obvious, but after spending entirely too much time on this, I thought I might ask here.</p>
  
  <p>Essentially, I have a large table (Large_table) that looks like this:</p>
  
  <pre><code>    nam startpos endpos  means File.Name
    12142 Chr 2        1  10000 0.1032  Strain_164
    12143 Chr 2    10001  20000 0.0097  Strain_164
    12144 Chr 2    20001  30000 0.0000  Strain_164
    12145 Chr 2    30001  40000 0.0000  Strain_164
    12146 Chr 2    40001  50000 0.0000  Strain_164
    12147 Chr 2    50001  60000 0.0000  Strain_164
    ...
    ...
    ...
    3240 Chr X 32390001 32400000 1.1921 Strain_98
    3241 Chr X 32400001 32410000 0.0827 Strain_98
    3242 Chr X 32410001 32420000 2.5432 Strain_98
    3243 Chr X 32420001 32430000 0.0404 Strain_98
    3244 Chr X 32430001 32440000 0.2218 Strain_98
    3245 Chr X 32440001 32450000 0.0645 Strain_98
  </code></pre>
  
  <p>What I have been trying to do is make a set of plots using ggplot and the facet_wrap option. The code for it is the following:</p>
  
  <pre><code>p &lt;- ggplot(data = Large_table, aes(x=startpos, y=means)) 
         + geom_point(aes(colour=nam), size = 2) 
         + coord_cartesian(ylim = c(0, 30)) + xlab("Chromosome Position (Mb)") 
         + ylab("Average Coverage per 10kb")
  p &lt;- p + theme(legend.position="none") 
         + scale_x_continuous(labels=function(x)x/1000000) 
         + ggtitle(y) + facet_grid(File.Name ~ nam , margins = T, scales="free_x", drop=T)
  p &lt;- p + theme(panel.background = element_rect(fill="white"), panel.margin=unit(1,"lines"))
  </code></pre>
  
  <p>I end up with a plot that looks like this:</p>
  
  <p><img src="https://i.stack.imgur.com/Y29OP.jpg" alt="Example of plots produced by ggplot"></p>
  
  <p>My issue is that I don't want the (all) column and row. I want only my data plotted, not the pooled results, and I don't know why ggplot is even making that. I looked at the help file but had no luck finding anything there either. I apologize again in advance because to me this seems like a really stupid question, but I cannot figure out why this is happening.</p>
  
  <p>Thank you</p>