title: R plot 2 axes multiple plots
body: <p>I'm trying to produce a very specific graphical output, and can't find a package that can do all of the things I'm looking for. Primarily, I need to:
  (1) Produce multiple plots (facet_wrap in ggplot works great)
  (2) Have 2 y-axes with different scales (lattice seems the best for this)
  (3) Produce a graph similar to the output from "plot" using dplR</p>
  
  <p>I have a data frame with multiple unique Sites. I'd like to plot each site's average annual value as a line graph, with a second line graph on the other y-axis representing sample depth. I'd like to produce a separate plot for each site.</p>
  
  <p>Below is some reproducible data(small subset), and what I've come up with so far:</p>
  
  <pre><code>&gt; sites &lt;- structure(list(Year = c("2009", "2009", "2009", "2009", "2009", 
  "2009", "2009", "2009", "2009", "2009", "2009", "2009", "2009", 
  "2009", "2009", "2009", "2009", "2009", "2009", "2009", "2009", 
  "2010", "2010", "2010", "2010", "2010", "2010", "2010", "2010", 
  "2010", "2010", "2010", "2010", "2010", "2010", "2010", "2010", 
  "2010", "2010", "2010", "2010", "2010", "2010", "2010", "2010", 
  "2011", "2011", "2011", "2011", "2011", "2011", "2011", "2011", 
  "2011", "2011", "2011", "2011", "2011", "2011", "2011", "2011", 
  "2011", "2011", "2011", "2011", "2011", "2011", "2012", "2012", 
  "2012"), plot = c("FA6", "FA7", "FK1", "FK2", "FK3", "FO1", "FO2", 
  "FO6", "GA2", "GA4", "GR1", "GR2", "HE2", "HE3", "LY1", "LY3", 
  "LY8", "NM2", "NM3", "TH3", "TH5", "BR1", "BR8", "FA5", "FA6", 
  "FA7", "FK1", "FK2", "FK3", "FO1", "FO2", "FO6", "GA2", "GA4", 
  "GR1", "GR2", "HE2", "HE3", "LY1", "LY3", "LY8", "NM2", "NM3", 
  "TH3", "TH5", "FA5", "FA6", "FA7", "FK1", "FK2", "FK3", "FO1", 
  "FO2", "FO6", "GA2", "GA4", "GR1", "GR2", "HE2", "HE3", "LY1", 
  "LY3", "LY8", "NM2", "NM3", "TH3", "TH5", "HE2", "HE3", "TH5"
  ), AvgRW = c(0.628666666666667, 0.485027777777778, 0.479269230769231, 
  0.826875, 0.633269230769231, 1.01830769230769, 1.34580555555556, 
  1.13061764705882, 0.422375, 1.377625, 0.535375, 0.366384615384615, 
  0.493119047619048, 0.300777777777778, 0.971923076923077, 1.02302941176471, 
  1.47245833333333, 1.00654166666667, 0.56425, 1.66342857142857, 
  1.28477586206897, 0.860666666666667, 2.10155130769231, 1.74626923076923, 
  0.616148148148148, 0.42775, 0.402576923076923, 0.859333333333333, 
  0.608961538461538, 1.28303846153846, 1.84344444444444, 1.52214705882353, 
  0.425546875, 1.66179166666667, 0.647208333333333, 0.390461538461538, 
  0.565892857142857, 0.237388888888889, 1.60419230769231, 1.16611764705882, 
  1.95329166666667, 1.18795833333333, 0.655928571428571, 2.009, 
  1.36198275862069, 2.61165384615385, 0.873296296296296, 0.596, 
  0.485884615384615, 1.13633333333333, 0.684461538461538, 1.30946153846154, 
  1.69747222222222, 1.64197058823529, 0.40740625, 1.40716666666667, 
  0.641625, 0.428576923076923, 0.729011904761905, 0.376222222222222, 
  1.52984615384615, 1.15317647058824, 1.66183333333333, 1.17904166666667, 
  0.604857142857143, 1.57425, 1.55772222222222, 0.7315, 0.119, 
  1.125875), SampDepth = c(27L, 18L, 13L, 12L, 13L, 13L, 18L, 17L, 
  32L, 12L, 12L, 13L, 14L, 18L, 13L, 17L, 12L, 12L, 14L, 14L, 29L, 
  21L, 13L, 13L, 27L, 18L, 13L, 12L, 13L, 13L, 18L, 17L, 32L, 12L, 
  12L, 13L, 14L, 18L, 13L, 17L, 12L, 12L, 14L, 14L, 29L, 13L, 27L, 
  18L, 13L, 12L, 13L, 13L, 18L, 17L, 32L, 12L, 12L, 13L, 14L, 18L, 
  13L, 17L, 12L, 12L, 14L, 4L, 9L, 2L, 1L, 8L)), .Names = c("Year", 
  "plot", "AvgRW", "SampDepth"), row.names = 2330:2399, class = "data.frame")
  </code></pre>
  
  <p>I can get a great layout using ggplot and ggplus, but can't seem to add second y-axis:</p>
  
  <pre><code>Plot1 &lt;- ggplot(sites,aes(x=Year, y=AvgRW, group=plot)) + 
      theme(axis.text=element_text(size=4), 
            panel.grid.minor=element_blank(), 
            panel.grid.major=element_line(colour = "gray",size=0.5), 
            strip.text=element_text(size=8)) + 
      geom_line()
  
  facet_multiple(plot = Plot1, facets = 'plot', ncol = 1, nrow = 1, scales="free")
  </code></pre>
  
  <p><a href="https://i.stack.imgur.com/jw11N.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/jw11N.jpg" alt="Sample graph"></a></p>
  
  <p>Then I tried doing a doubleYplot with lattice and latticeExtra, but I can't get the lines to appear:</p>
  
  <pre><code>Plot2a &lt;- xyplot(AvgRW ~ Year, data=sites, groups=plot,
                xlab=list("Year", fontsize = 12),
                ylab = list("Avg RW (mm)", fontsize = 12),
                ylab.right = list("Sample Depth", fontsize = 12),
                par.settings = simpleTheme(col = 1),
                type = c("l","g"),
                lty=1,
                scales=list(x=list(rot=90,tick.number=25,
                                   cex=1,axs="r")))
  
  &gt; Plot2b &lt;- xyplot(SampDepth ~ Year,data=sites, groups=plot, type = "o",col="black",
                lty=9)
  
  &gt; doubleYScale(Plot2a, Plot2b)
  </code></pre>
  
  <p>My ultimate goal is to produce a graph that looks similar to the dplR output, for every site in my data.frame:</p>
  
  <p><a href="https://i.stack.imgur.com/aGmcy.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/aGmcy.jpg" alt="Intended output"></a></p>
  
  <p>Any ideas on how to combine my three goals would be greatly appreciated.</p>