Hello,

I am trying to generate a set of boxplots using ggplot with the following
data with 4 columns (Day, Site, VO2, Cruise)

 AllCorbulaMR
    Day Site          VO2 Cruise
1     1    1 148.43632670      1
2     1    1  61.73864969      1
3     1    1  92.64536096      1
4     1    1  73.35434957      1
5     1    1  69.85568810      1
6     1    1  98.71116866      1
7     1    1  67.57880107      1
8     1    1  80.57959160      1
9     1    1  53.38577137      1
10    1    2  81.08429594      1
11    1    2  79.73019687      1
12    1    2  67.93991806      1
13    1    2  50.69929558      1
14    1    2  42.02457680      1
15    1    2  64.10049924      1
16    1    2  80.02264095      1
17    1    2  67.14828804      1
18    1    2  93.33363743      1
19    1    3  53.86021985      1
20    1    3  50.53366868      1
21    1    3  52.12437086      1
22    1    3  43.44618922      1
23    1    3  64.64322840      1
24    1    3  55.03761768      1
25    1    3  67.79501374      1
26    1    4  12.70806068      1
27    1    4 114.56401960      1
28    1    4  34.34450695      1
29    1    4  76.70849935      1
30    1    4  68.99752863      1
31    1    4  71.23080332      1
32    1    1   0.08222308      2
33    1    1           NA      2
34    1    1   0.03743258      2
35    1    1   0.04496363      2
36    1    1   0.07184903      2
37    1    1   0.05637676      2
38    1    1   0.05163886      2
39    1    1   0.03022606      2
40    1    1   0.04150667      2
41    2    1   0.04982530      2
42    2    1   0.05248479      2
43    2    1   0.03839707      2
44    2    1   0.04283591      2
45    2    1   0.03285247      2
46    2    1   0.03965853      2
47    2    1           NA      2
48    2    1   0.03637822      2
49    2    1   0.03686663      2
50    1    2   0.04086229      2
51    1    2           NA      2
52    1    2   0.01891389      2
53    1    2   0.03365864      2
54    1    2   0.04179611      2
55    1    2   0.04675111      2
56    1    2   0.04734616      2
57    1    2   0.04046907      2
58    1    2   0.03395499      2
59    2    2   0.02104620      2
60    2    2           NA      2
61    2    2           NA      2
62    2    2           NA      2
63    2    2   0.01882796      2
64    2    2           NA      2
65    2    2           NA      2
66    2    2   0.02328894      2
67    2    2   0.02635327      2
68    1    3   0.06030056      2
69    1    3   0.04728888      2
70    1    3   0.04307900      2
71    1    3   0.05144241      2
72    1    3   0.03223973      2
73    1    3   0.05145292      2
74    1    3   0.02718536      2
75    1    3   0.02830348      2
76    1    3   0.05859836      2
77    2    3   0.04521778      2
78    2    3   0.03242385      2
79    2    3   0.03412688      2
80    2    3   0.04407171      2
81    2    3   0.04517834      2
82    2    3           NA      2
83    2    3   0.02745407      2
84    2    3   0.03118602      2
85    2    3   0.04420074      2
86    1    4   0.05352334      2
87    1    4   0.05378120      2
88    1    4   0.04394838      2
89    1    4   0.02597939      2
90    1    4   0.05476946      2
91    1    4   0.04371743      2
92    2    4   0.04022729      2
93    2    4   0.04078509      2
94    2    4   0.04911994      2
95    2    4   0.04068468      2
96    2    4           NA      2
97    2    4           NA      2
98    1    1   0.08892223      3
99    1    1   0.08617873      3
100   1    1   0.06108950      3
101   1    1   0.19047922      3
102   1    1   0.09865930      3
103   1    1   0.12103549      3
104   1    1   0.06788404      3
105   1    1   0.12629497      3
106   1    1   0.10947173      3
107   1    1   0.11381467      3
108   2    1   0.07809781      3
109   2    1   0.04397586      3
110   2    1   0.06317635      3
111   2    1   0.02020365      3
112   2    1   0.09525985      3
113   2    1   0.04732347      3
114   2    1   0.03043341      3
115   2    1   0.04419395      3
116   2    1           NA      3
117   2    1           NA      3
118   1    2   0.03380003      3
119   1    2   0.02600926      3
120   1    2   0.03980552      3
121   1    2   0.03659985      3
122   1    2   0.04867881      3
123   1    2   0.03694679      3
124   1    2   0.03372825      3
125   1    2   0.03644750      3
126   1    2   0.01497611      3
127   1    2   0.02697976      3
128   2    2   0.03136923      3
129   2    2   0.03602215      3
130   2    2   0.04000660      3
131   2    2   0.03673098      3
132   2    2   0.03090854      3
133   2    2   0.04877643      3
134   2    2   0.02468537      3
135   2    2           NA      3
136   2    2           NA      3
137   2    2           NA      3
138   1    3   0.04809866      3
139   1    3   0.02380070      3
140   1    3   0.03672271      3
141   1    3   0.03232115      3
142   1    3   0.02950701      3
143   1    3   0.05068163      3
144   1    3   0.03004234      3
145   1    3   0.03090461      3
146   1    3   0.04539888      3
147   1    3   0.03261571      3
148   2    3   0.02069708      3
149   2    3   0.02117658      3
150   2    3   0.03244907      3
151   2    3   0.03404048      3
152   2    3   0.04597381      3
153   2    3   0.04034278      3
154   2    3   0.02167128      3
155   2    3   0.02245179      3
156   2    3           NA      3
157   2    3           NA      3
158   1    4   0.03935839      3
159   1    4   0.02932294      3
160   1    4   0.04928409      3
161   1    4   0.05075344      3
162   1    4   0.04353663      3
163   1    4   0.03376173      3
164   1    4   0.03640901      3
165   1    4   0.03616992      3
166   1    4   0.04999144      3
167   1    4           NA      3
168   2    4   0.02864131      3
169   2    4   0.02269317      3
170   2    4   0.04231203      3
171   2    4   0.03117968      3
172   2    4   0.05936813      3
173   2    4   0.04453866      3
174   2    4   0.04596834      3
175   2    4   0.03316604      3
176   2    4   0.03557714      3
177   2    4   0.03546922      3
178   1    1  25.85293219      4
179   1    1 114.35190440      4
180   1    1  41.24654852      4
181   1    1  30.41020474      4
182   1    1  36.48809050      4
183   1    1  54.41756532      4
184   1    1  19.80251528      4
185   1    1  69.26706620      4
186   1    1  24.58416429      4
187   1    1  34.07847862      4
188   2    1  21.89169319      4
189   2    1  59.63530232      4
190   2    1  18.52010709      4
191   2    1  41.19883744      4
192   2    1  48.19844111      4
193   2    1  15.39495989      4
194   2    1  29.50623201      4
195   2    1  51.30763254      4
196   2    1   7.47325378      4
197   2    1  24.31193857      4
198   1    2  19.29834204      4
199   1    2  36.58998998      4
200   1    2  28.68983063      4
201   1    2  67.06563511      4
202   1    2  30.00310234      4
203   1    2  28.28411410      4
204   1    2  34.81315669      4
205   1    2  45.49758389      4
206   1    2  30.96530199      4
207   1    2  35.12478034      4
208   2    2  20.10730199      4
209   2    2  20.51722925      4
210   2    2   0.74851863      4
211   2    2  16.93243539      4
212   2    2   8.88325120      4
213   2    2  49.09739859      4
214   2    2   6.19244047      4
215   2    2  27.52476529      4
216   2    2  14.38173305      4
217   2    2   5.80964158      4
218   1    3  29.04103986      4
219   1    3   0.92325019      4
220   1    3  29.13337158      4
221   1    3  34.74658994      4
222   1    3  49.14354727      4
223   1    3  22.07507554      4
224   1    3  34.33727406      4
225   1    3  36.87618286      4
226   1    3  31.18096886      4
227   1    3  36.55777870      4
228   2    3  25.58876028      4
229   2    3   0.98494566      4
230   2    3  24.97630908      4
231   2    3  11.95195819      4
232   2    3  21.70297861      4
233   2    3  13.65235649      4
234   2    3  10.50488380      4
235   2    3   2.87966024      4
236   2    3   2.73826233      4
237   2    3   0.11720351      4
238   1    4   4.55652677      4
239   1    4   8.70352253      4
240   1    4  41.11933137      4
241   1    4  28.85120068      4
242   1    4  32.32787505      4
243   1    4  23.07206283      4
244   1    4  21.14382198      4
245   1    4  13.81868580      4
246   1    4  58.54591722      4
247   1    4  43.80195253      4
248   2    4  46.78384255      4
249   2    4   0.61816630      4
250   2    4  13.55381496      4
251   2    4   4.48444064      4
252   2    4  14.19295226      4
253   2    4  11.94361059      4
254   2    4  35.62088407      4
255   2    4  16.11595544      4
256   2    4  34.80256181      4
257   2    4  19.66686930      4

I would like to make a boxplot with Site on the x-axis and VO2 on the y-axis
and with the fill colour specified by the Cruise. I have the following code

p=ggplot(AllCorbulaMR,aes(factor(Site),VO2))

p+geom_boxplot(aes(fill=factor(Cruise)))+scale_fill_manual('Cruise',
values=(colours()[c(375,577,573,439)]), breaks=c(1,2,3,4), labels=c('Cruise
1', 'Cruise 2', 'Cruise 3', 'Cruise 4'))+xlab('Sampling
Site')+ylab(expression("Metabolic Rate  "
(mu*moles*~O[2]*~mg^-1*~hr^-1)))+opts(title="Corbula
Cruises")+ylim(c(0,0.2))


The issue I have at the moment is that only Cruises 2 and 3 are plotted
correctly. The other two are not shown or the boxes are plotted as single
horizontal lines. I also get a warning that 129 rows containing missing data
were removed (probably explaining the missing boxplots). I have a few
missing data points (specified NA), but not 129. Can anyone see an error in
the code I have that would explain why some rows of data are being
disregarded?

Thank you,

Nate

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