title: Faceting by 2 factors in ggplot2
body: <p>I have the following data set and code and have also showed the output from dput().  I want to plot the log(N2012$Rate) column on the y axis with Location on the x axis and faceted vertically by Month and horizontally by Gas.  The graph works visually but is not assigning the correct data points to the factors.  I'm not sure what I'm doing incorrectly.  Sorry for the clumsy code, I'm new to R and have taught myself.</p>
  
  <p>I also want the N2O panels to be yellow and the N2 panels blue.  That's also not happening and I'm not sure why.</p>
  
  <p>Data</p>
  
  <pre><code>    Location.Month Gas     Rate Month Location log(N2012$Rate)
  1   HighBank July  N2    24.00  July HighBank       3.1780538
  2   HighBank July  N2   309.00  July HighBank       5.7333413
  3   HighBank July N2O    92.00  July HighBank       4.5217886
  4   HighBank July N2O    45.00  July HighBank       3.8066625
  5    LowBank July  N2   582.00  July  LowBank       6.3664704
  6    LowBank July  N2    27.00  July  LowBank       3.2958369
  7    LowBank July N2O   299.00  July  LowBank       5.7004436
  8    LowBank July N2O    99.00  July  LowBank       4.5951199
  9      Basin July  N2   219.00  July    Basin       5.3890717
  10     Basin July  N2  1096.00  July    Basin       6.9994225
  11     Basin July  N2   151.00  July    Basin       5.0172798
  12     Basin July  N2   326.00  July    Basin       5.7868974
  13     Basin July  N2   135.00  July    Basin       4.9052748
  14     Basin July  N2    29.00  July    Basin       3.3672958
  15     Basin July  N2   140.00  July    Basin       4.9416424
  16     Basin July N2O   124.00  July    Basin       4.8202816
  17     Basin July N2O    97.00  July    Basin       4.5747110
  18     Basin July N2O   177.00  July    Basin       5.1761497
  19     Basin July N2O   702.00  July    Basin       6.5539334
  20     Basin July N2O   202.00  July    Basin       5.3082677
  21     Basin July N2O    76.00  July    Basin       4.3307333
  22     Basin July N2O    51.00  July    Basin       3.9318256
  23   HighBank Aug  N2  2328.00   Aug HighBank       7.7527648
  24   HighBank Aug  N2   584.00   Aug HighBank       6.3699010
  25   HighBank Aug N2O  1137.00   Aug HighBank       7.0361485
  26   HighBank Aug N2O  1438.00   Aug HighBank       7.2710085
  27    LowBank Aug  N2   217.00   Aug  LowBank       5.3798974
  28    LowBank Aug  N2   947.00   Aug  LowBank       6.8532991
  29    LowBank Aug N2O   398.00   Aug  LowBank       5.9864520
  30    LowBank Aug N2O   984.00   Aug  LowBank       6.8916259
  31      Basin Aug  N2   787.00   Aug    Basin       6.6682282
  32      Basin Aug  N2   365.00   Aug    Basin       5.8998974
  33      Basin Aug  N2   597.00   Aug    Basin       6.3919171
  34      Basin Aug  N2  6125.00   Aug    Basin       8.7201340
  35      Basin Aug  N2 13439.00   Aug    Basin       9.5059162
  36      Basin Aug  N2  9348.00   Aug    Basin       9.1429177
  37      Basin Aug  N2  8679.00   Aug    Basin       9.0686616
  38      Basin Aug N2O  1177.00   Aug    Basin       7.0707241
  39      Basin Aug N2O   119.00   Aug    Basin       4.7791235
  40      Basin Aug N2O   182.00   Aug    Basin       5.2040067
  41      Basin Aug N2O   352.00   Aug    Basin       5.8636312
  42      Basin Aug N2O  4051.00   Aug    Basin       8.3067190
  43      Basin Aug N2O  1921.00   Aug    Basin       7.5606012
  44      Basin Aug N2O  2017.00   Aug    Basin       7.6093665
  45  HighBank Sept  N2    25.70  Sept HighBank       3.2464910
  46  HighBank Sept  N2    28.30  Sept HighBank       3.3428618
  47  HighBank Sept N2O    17.70  Sept HighBank       2.8735646
  48  HighBank Sept N2O   157.00  Sept HighBank       5.0562458
  49   LowBank Sept  N2     6.19  Sept  LowBank       1.8229351
  50   LowBank Sept  N2    67.60  Sept  LowBank       4.2136080
  51   LowBank Sept N2O     9.51  Sept  LowBank       2.2523439
  52   LowBank Sept N2O   244.00  Sept  LowBank       5.4971682
  53     Basin Sept  N2  1077.00  Sept    Basin       6.9819347
  54     Basin Sept  N2   160.00  Sept    Basin       5.0751738
  55     Basin Sept  N2   949.00  Sept    Basin       6.8554088
  56     Basin Sept  N2   714.00  Sept    Basin       6.5708830
  57     Basin Sept  N2    28.30  Sept    Basin       3.3428618
  58     Basin Sept  N2  1838.00  Sept    Basin       7.5164333
  59     Basin Sept  N2   249.00  Sept    Basin       5.5174529
  60     Basin Sept N2O   397.00  Sept    Basin       5.9839363
  61     Basin Sept N2O   197.00  Sept    Basin       5.2832037
  62     Basin Sept N2O   366.00  Sept    Basin       5.9026333
  63     Basin Sept N2O    27.60  Sept    Basin       3.3178158
  64     Basin Sept N2O    44.20  Sept    Basin       3.7887248
  65     Basin Sept N2O   112.00  Sept    Basin       4.7184989
  66     Basin Sept N2O   171.00  Sept    Basin       5.1416636
  67   HighBank Oct  N2     9.43   Oct HighBank       2.2438961
  68   HighBank Oct  N2     3.77   Oct HighBank       1.3270750
  69   HighBank Oct N2O     3.13   Oct HighBank       1.1410330
  70   HighBank Oct N2O    19.10   Oct HighBank       2.9496883
  71    LowBank Oct  N2     2.39   Oct  LowBank       0.8712934
  72    LowBank Oct  N2     5.66   Oct  LowBank       1.7334239
  73    LowBank Oct N2O    40.20   Oct  LowBank       3.6938670
  74    LowBank Oct N2O    27.80   Oct  LowBank       3.3250360
  75      Basin Oct  N2    55.60   Oct    Basin       4.0181832
  76      Basin Oct  N2    20.20   Oct    Basin       3.0056826
  77      Basin Oct  N2    55.20   Oct    Basin       4.0109630
  78      Basin Oct  N2     8.90   Oct    Basin       2.1860513
  79      Basin Oct  N2     3.72   Oct    Basin       1.3137237
  80      Basin Oct  N2     9.06   Oct    Basin       2.2038691
  81      Basin Oct  N2     8.04   Oct    Basin       2.0844291
  82      Basin Oct N2O    25.50   Oct    Basin       3.2386785
  83      Basin Oct N2O    29.30   Oct    Basin       3.3775875
  84      Basin Oct N2O    16.90   Oct    Basin       2.8273136
  85      Basin Oct N2O     5.17   Oct    Basin       1.6428727
  86      Basin Oct N2O     6.33   Oct    Basin       1.8453002
  87      Basin Oct N2O     7.72   Oct    Basin       2.0438144
  88      Basin Oct N2O     7.58   Oct    Basin       2.0255132
  </code></pre>
  
  <p>Data structure</p>
  
  <pre><code>Data &lt;-
  structure(list(Location.Month = structure(c(6L, 6L, 6L, 6L, 10L, 
  10L, 10L, 10L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
  2L, 2L, 5L, 5L, 5L, 5L, 9L, 9L, 9L, 9L, 1L, 1L, 1L, 1L, 1L, 1L, 
  1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 8L, 8L, 8L, 8L, 12L, 12L, 12L, 
  12L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
  7L, 7L, 7L, 7L, 11L, 11L, 11L, 11L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
  3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = c("Basin Aug", "Basin July", 
  "Basin Oct", "Basin Sept", "HighBank Aug", "HighBank July", "HighBank Oct", 
  "HighBank Sept", "LowBank Aug", "LowBank July", "LowBank Oct", 
  "LowBank Sept"), class = "factor"), Gas = structure(c(1L, 1L, 
  2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 
  2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 
  1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 
  2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
  1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 
  2L, 2L, 2L, 2L, 2L, 2L), .Label = c("N2", "N2O"), class = "factor"), 
      Rate = c(24, 309, 92, 45, 582, 27, 299, 99, 219, 1096, 151, 
      326, 135, 29, 140, 124, 97, 177, 702, 202, 76, 51, 2328, 
      584, 1137, 1438, 217, 947, 398, 984, 787, 365, 597, 6125, 
      13439, 9348, 8679, 1177, 119, 182, 352, 4051, 1921, 2017, 
      25.7, 28.3, 17.7, 157, 6.19, 67.6, 9.51, 244, 1077, 160, 
      949, 714, 28.3, 1838, 249, 397, 197, 366, 27.6, 44.2, 112, 
      171, 9.43, 3.77, 3.13, 19.1, 2.39, 5.66, 40.2, 27.8, 55.6, 
      20.2, 55.2, 8.9, 3.72, 9.06, 8.04, 25.5, 29.3, 16.9, 5.17, 
      6.33, 7.72, 7.58), Month = structure(c(1L, 1L, 1L, 1L, 1L, 
      1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
      1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
      2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 
      3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
      3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
      4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L), .Label = c("July", "Aug", 
      "Sept", "Oct"), class = "factor"), Location = structure(c(1L, 
      1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
      3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 
      3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 
      1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
      3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 
      3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = c("HighBank", 
      "LowBank", "Basin"), class = "factor"), `log(N2012$Rate)` = c(3.17805383034795, 
      5.73334127689775, 4.52178857704904, 3.80666248977032, 6.36647044773144, 
      3.29583686600433, 5.70044357339069, 4.59511985013459, 5.3890717298165, 
      6.99942246750796, 5.01727983681492, 5.78689738136671, 4.90527477843843, 
      3.36729582998647, 4.9416424226093, 4.82028156560504, 4.57471097850338, 
      5.17614973257383, 6.55393340402581, 5.30826769740121, 4.33073334028633, 
      3.93182563272433, 7.75276480885133, 6.36990098282823, 7.03614849375054, 
      7.27100853828099, 5.37989735354046, 6.85329909318608, 5.98645200528444, 
      6.89162589705225, 6.6682282484174, 5.89989735358249, 6.3919171133926, 
      8.72013403541293, 9.50591620654706, 9.14291769565875, 9.06866159364425, 
      7.07072410726028, 4.77912349311153, 5.2040066870768, 5.8636311755981, 
      8.30671904320269, 7.56060116276856, 7.60936653795421, 3.24649099190117, 
      3.34286180464919, 2.87356463957978, 5.05624580534831, 1.8229350866965, 
      4.21360798304892, 2.2523438765573, 5.4971682252932, 6.98193467715639, 
      5.07517381523383, 6.85540879860993, 6.57088296233958, 3.34286180464919, 
      7.51643330291563, 5.51745289646471, 5.98393628068719, 5.28320372873799, 
      5.90263333340137, 3.3178157727231, 3.78872478908365, 4.71849887129509, 
      5.14166355650266, 2.24389609664537, 1.32707500145992, 1.14103300455206, 
      2.94968833505258, 0.871293365943419, 1.73342389221509, 3.69386699562498, 
      3.32503602069659, 4.01818320125654, 3.00568260440716, 4.01096295328305, 
      2.18605127673809, 1.31372366828506, 2.20386912005489, 2.08442908319087, 
      3.23867845216438, 3.37758751602302, 2.82731362192903, 1.64287268852034, 
      1.84530023615608, 2.04381436403668, 2.02551319965428)), .Names = c("Location.Month", 
  "Gas", "Rate", "Month", "Location", "log(N2012$Rate)"), row.names = c(NA, 
  -88L), class = "data.frame")
  </code></pre>
  
  <p>Code</p>
  
  <pre><code>Data$Location = factor(Data$Location,c("HighBank", "LowBank", "Basin"))
  Data$Gas = factor(Data$Gas,c("N2", "N2O"))
  colvec&lt;-c("blue", "yellow")
  Data$Month = factor(Data$Month,c("July", "Aug", "Sept", "Oct"))
  p &lt;- ggplot(Data, aes(factor(Location),log(N2012$Rate), factor(Gas)))
  pl &lt;- p + geom_boxplot(fill="blue", width = 0.7) + geom_point()  
  plo &lt;- pl + scale_fill_manual(values=colvec) + facet_grid(Gas ~ Month)
  plot &lt;- plo + xlab("Location") + ylab("log(N2O ug N2O-N/m2/h)")  
  plots &lt;-plot + theme(axis.title.x = element_text(face="bold", colour="Black", size=15),
         axis.text.x  = element_text(angle=50, vjust=0.5, size=12, colour="Black"), 
      axis.title.y = element_text(face="bold", size=13), 
      axis.text.y = element_text(size=12, colour="black"))
  plots
  </code></pre>
  
  <p>Thanks,</p>
  
  <p>-Sarah</p>