Isaac Isaac - 20 days ago 6
R Question

R/ggplot2 -- facet by day, plotting in the wrong order

I am trying to plot some time series data and facet it by day. I have no trouble managing the facets, but cannot understand why the x-axis for each day is not in the right order. That is, instead of starting at 0:00 and ending at 23:59, it's starting at 22:00 and ending at 22:00. Any help greatly appreciated:

enter image description here

#Convert Datetime column to R POSIXct
original_data$Date<-as.POSIXct(x = original_data$Date, format = "%m/%d/%Y %H:%M")

#Set reference values to numeric
original_data$Reference<-as.numeric(original_data$Reference)

calibration_plot<-ggplot(original_data, aes(Date, Reference)) +
facet_wrap(~DOY, scales = "free") + xlab("Time (hours)") +
geom_point()+ ylab(expression(Radiation ~ (W ~ m^{-2}))) +
scale_x_datetime(labels = date_format("%H")) + ggtitle("Calibration
Plots") + theme_bw() + theme(axis.text=element_text(size=12),
axis.title=element_text(size=12,face="bold"), title =
element_text(size=10, face = "bold"))


Date DOY Reference
11/7/2016 0:01 312 -0.0137
11/7/2016 0:06 312 -0.01525
11/7/2016 0:11 312 -0.01325
11/7/2016 0:16 312 -0.01235
11/7/2016 0:21 312 -0.0119
11/7/2016 0:26 312 -0.0112
11/7/2016 0:31 312 -0.0109
11/7/2016 0:36 312 -0.0112
11/7/2016 0:41 312 -0.0105
11/7/2016 0:46 312 -0.00865
11/7/2016 0:51 312 -0.00875
11/7/2016 0:56 312 -0.0081
11/7/2016 1:01 312 -0.00885
11/7/2016 1:06 312 -0.00775
11/7/2016 1:11 312 -0.0086
11/7/2016 1:16 312 -0.0085
11/7/2016 1:21 312 -0.00915
11/7/2016 1:26 312 -0.0077
11/7/2016 1:31 312 -0.0114
11/7/2016 1:36 312 -0.0148
11/7/2016 1:41 312 -0.0121
11/7/2016 1:46 312 -0.012
11/7/2016 1:51 312 -0.0121
11/7/2016 1:56 312 -0.0086
11/7/2016 2:01 312 -0.00915
11/7/2016 2:06 312 -0.00945
11/7/2016 2:11 312 -0.0072
11/7/2016 2:16 312 -0.00485
11/7/2016 2:21 312 -0.006
11/7/2016 2:26 312 -0.00605
11/7/2016 2:31 312 -0.00685
11/7/2016 2:36 312 -0.00905
11/7/2016 2:41 312 -0.01085
11/7/2016 2:46 312 -0.0133
11/7/2016 2:51 312 -0.0118
11/7/2016 2:56 312 -0.01285
11/7/2016 3:01 312 -0.0125
11/7/2016 3:06 312 -0.0108
11/7/2016 3:11 312 -0.0114
11/7/2016 3:16 312 -0.01165
11/7/2016 3:21 312 -0.0117
11/7/2016 3:26 312 -0.0116
11/7/2016 3:31 312 -0.01155
11/7/2016 3:36 312 -0.01345
11/7/2016 3:41 312 -0.01375
11/7/2016 3:46 312 -0.01405
11/7/2016 3:51 312 -0.01195
11/7/2016 3:56 312 -0.012
11/7/2016 4:01 312 -0.0115
11/7/2016 4:06 312 -0.01215
11/7/2016 4:11 312 -0.01155
11/7/2016 4:16 312 -0.013
11/7/2016 4:21 312 -0.01135
11/7/2016 4:26 312 -0.01165
11/7/2016 4:31 312 -0.01125
11/7/2016 4:36 312 -0.01025
11/7/2016 4:41 312 -0.0106
11/7/2016 4:46 312 -0.0118
11/7/2016 4:51 312 -0.01045
11/7/2016 4:56 312 -0.0108
11/7/2016 5:01 312 -0.01315
11/7/2016 5:06 312 -0.01155
11/7/2016 5:11 312 -0.01195
11/7/2016 5:16 312 -0.01255
11/7/2016 5:21 312 -0.01145
11/7/2016 5:26 312 -0.011
11/7/2016 5:31 312 -0.0108
11/7/2016 5:36 312 -0.01115
11/7/2016 5:41 312 -0.0104
11/7/2016 5:46 312 -0.00325
11/7/2016 5:51 312 0.01585
11/7/2016 5:56 312 0.0383
11/7/2016 6:01 312 0.0541
11/7/2016 6:06 312 0.08845
11/7/2016 6:11 312 0.16495
11/7/2016 6:16 312 0.2525
11/7/2016 6:21 312 0.3453
11/7/2016 6:26 312 0.4411
11/7/2016 6:31 312 0.5581
11/7/2016 6:36 312 0.73945
11/7/2016 6:41 312 0.84045
11/7/2016 6:46 312 1.0619
11/7/2016 6:51 312 1.50535
11/7/2016 6:56 312 1.7774
11/7/2016 7:01 312 1.9699
11/7/2016 7:06 312 1.94915
11/7/2016 7:11 312 1.984
11/7/2016 7:16 312 2.17855
11/7/2016 7:21 312 2.5005
11/7/2016 7:26 312 2.35345
11/7/2016 7:31 312 2.43305
11/7/2016 7:36 312 2.63425
11/7/2016 7:41 312 3.16065
11/7/2016 7:46 312 3.34475
11/7/2016 7:51 312 3.2605
11/7/2016 7:56 312 3.3372
11/7/2016 8:01 312 3.3398
11/7/2016 8:06 312 3.43235
11/7/2016 8:11 312 3.8922
11/7/2016 8:16 312 4.359
11/7/2016 8:21 312 4.4112
11/7/2016 8:26 312 4.7168
11/7/2016 8:31 312 4.8878
11/7/2016 8:36 312 5.05045
11/7/2016 8:41 312 5.20745
11/7/2016 8:46 312 4.82285
11/7/2016 8:51 312 5.19705
11/7/2016 8:56 312 4.9623
11/7/2016 9:01 312 5.164
11/7/2016 9:06 312 5.85755
11/7/2016 9:11 312 5.91635
11/7/2016 9:16 312 6.20635
11/7/2016 9:21 312 6.3367
11/7/2016 9:26 312 6.4511
11/7/2016 9:31 312 6.5009
11/7/2016 9:36 312 6.55115
11/7/2016 9:41 312 6.77255
11/7/2016 9:46 312 6.73385
11/7/2016 9:51 312 6.739
11/7/2016 9:56 312 7.0979
11/7/2016 10:01 312 7.2608
11/7/2016 10:06 312 7.39525
11/7/2016 10:11 312 7.32865
11/7/2016 10:16 312 7.4016
11/7/2016 10:21 312 7.70725
11/7/2016 10:26 312 7.8645
11/7/2016 10:31 312 7.8682
11/7/2016 10:36 312 8.0161
11/7/2016 10:41 312 7.7934
11/7/2016 10:46 312 5.99495
11/7/2016 10:51 312 8.25685
11/7/2016 10:56 312 8.7265
11/7/2016 11:01 312 8.5505
11/7/2016 11:06 312 8.1372
11/7/2016 11:11 312 5.0642
11/7/2016 11:16 312 5.0355
11/7/2016 11:21 312 6.32535
11/7/2016 11:26 312 5.8676
11/7/2016 11:31 312 7.37175
11/7/2016 11:36 312 6.1949
11/7/2016 11:41 312 5.01225
11/7/2016 11:46 312 5.91725
11/7/2016 11:51 312 6.7572
11/7/2016 11:56 312 7.70375
11/7/2016 12:01 312 8.12815
11/7/2016 12:06 312 6.04805
11/7/2016 12:11 312 5.2638
11/7/2016 12:16 312 4.85
11/7/2016 12:21 312 4.2291
11/7/2016 12:26 312 4.2851
11/7/2016 12:31 312 4.99735
11/7/2016 12:36 312 4.7308
11/7/2016 12:41 312 5.2383
11/7/2016 12:46 312 6.9894
11/7/2016 12:51 312 6.8357
11/7/2016 12:56 312 9.124
11/7/2016 13:01 312 9.2875
11/7/2016 13:06 312 7.11615
11/7/2016 13:11 312 7.8034
11/7/2016 13:16 312 5.29235
11/7/2016 13:21 312 6.02785
11/7/2016 13:26 312 5.6154
11/7/2016 13:31 312 3.5963
11/7/2016 13:36 312 2.88325
11/7/2016 13:41 312 2.7976
11/7/2016 13:46 312 3.07845
11/7/2016 13:51 312 3.55455
11/7/2016 13:56 312 3.2716
11/7/2016 14:01 312 2.8856
11/7/2016 14:06 312 4.42685
11/7/2016 14:11 312 6.93045
11/7/2016 14:16 312 6.68565
11/7/2016 14:21 312 6.0181
11/7/2016 14:26 312 3.3964
11/7/2016 14:31 312 3.3697
11/7/2016 14:36 312 2.99275
11/7/2016 14:41 312 5.2926
11/7/2016 14:46 312 4.70665
11/7/2016 14:51 312 4.16065
11/7/2016 14:56 312 3.7451
11/7/2016 15:01 312 3.47665
11/7/2016 15:06 312 3.2893
11/7/2016 15:11 312 3.0863
11/7/2016 15:16 312 2.9122
11/7/2016 15:21 312 2.71525
11/7/2016 15:26 312 2.50645
11/7/2016 15:31 312 2.26005
11/7/2016 15:36 312 2.0562
11/7/2016 15:41 312 1.89285
11/7/2016 15:46 312 1.3635
11/7/2016 15:51 312 1.1739
11/7/2016 15:56 312 1.4291
11/7/2016 16:01 312 1.1776
11/7/2016 16:06 312 1.03155
11/7/2016 16:11 312 0.8916
11/7/2016 16:16 312 0.73225
11/7/2016 16:21 312 0.6009
11/7/2016 16:26 312 0.47795
11/7/2016 16:31 312 0.35235
11/7/2016 16:36 312 0.2142
11/7/2016 16:41 312 0.11565
11/7/2016 16:46 312 0.04355
11/7/2016 16:51 312 0.0127
11/7/2016 16:56 312 -0.00405
11/7/2016 17:01 312 -0.0198
11/7/2016 17:06 312 -0.02375
11/7/2016 17:11 312 -0.0219
11/7/2016 17:16 312 -0.01975
11/7/2016 17:21 312 -0.02105
11/7/2016 17:26 312 -0.02275
11/7/2016 17:31 312 -0.022
11/7/2016 17:36 312 -0.02135
11/7/2016 17:41 312 -0.02165
11/7/2016 17:46 312 -0.0232
11/7/2016 17:51 312 -0.01995
11/7/2016 17:56 312 -0.02085
11/7/2016 18:01 312 -0.0197
11/7/2016 18:06 312 -0.02185
11/7/2016 18:11 312 -0.0213
11/7/2016 18:16 312 -0.022
11/7/2016 18:21 312 -0.01915
11/7/2016 18:26 312 -0.0211
11/7/2016 18:31 312 -0.02025
11/7/2016 18:36 312 -0.0198
11/7/2016 18:41 312 -0.0205
11/7/2016 18:46 312 -0.0212
11/7/2016 18:51 312 -0.0212
11/7/2016 18:56 312 -0.0221
11/7/2016 19:01 312 -0.0209
11/7/2016 19:06 312 -0.0214
11/7/2016 19:11 312 -0.02025
11/7/2016 19:16 312 -0.02115
11/7/2016 19:21 312 -0.02205
11/7/2016 19:26 312 -0.0225
11/7/2016 19:31 312 -0.0216
11/7/2016 19:36 312 -0.0206
11/7/2016 19:41 312 -0.02145
11/7/2016 19:46 312 -0.0214
11/7/2016 19:51 312 -0.02115
11/7/2016 19:56 312 -0.021
11/7/2016 20:01 312 -0.02075
11/7/2016 20:06 312 -0.0224
11/7/2016 20:11 312 -0.02035
11/7/2016 20:16 312 -0.01915
11/7/2016 20:21 312 -0.02075
11/7/2016 20:26 312 -0.02095
11/7/2016 20:31 312 -0.0228
11/7/2016 20:36 312 -0.0207
11/7/2016 20:41 312 -0.0215
11/7/2016 20:46 312 -0.01995
11/7/2016 20:51 312 -0.0209
11/7/2016 20:56 312 -0.0202
11/7/2016 21:01 312 -0.02125
11/7/2016 21:06 312 -0.02045
11/7/2016 21:11 312 -0.02345
11/7/2016 21:16 312 -0.02325
11/7/2016 21:21 312 -0.02195
11/7/2016 21:26 312 -0.02065
11/7/2016 21:31 312 -0.01935
11/7/2016 21:36 312 -0.01475
11/7/2016 21:41 312 -0.0172
11/7/2016 21:46 312 -0.01635
11/7/2016 21:51 312 -0.01495
11/7/2016 21:56 312 -0.0145
11/7/2016 22:01 312 -0.0177
11/7/2016 22:06 312 -0.01585
11/7/2016 22:11 312 -0.0134
11/7/2016 22:16 312 -0.01355
11/7/2016 22:21 312 -0.01435
11/7/2016 22:26 312 -0.0134
11/7/2016 22:31 312 -0.0157
11/7/2016 22:36 312 -0.01535
11/7/2016 22:41 312 -0.0139
11/7/2016 22:46 312 -0.01495
11/7/2016 22:51 312 -0.01585
11/7/2016 22:56 312 -0.01735
11/7/2016 23:01 312 -0.01475
11/7/2016 23:06 312 -0.0165
11/7/2016 23:11 312 -0.0157
11/7/2016 23:16 312 -0.0223
11/7/2016 23:21 312 -0.0214
11/7/2016 23:26 312 -0.02155
11/7/2016 23:31 312 -0.02245
11/7/2016 23:36 312 -0.0223
11/7/2016 23:41 312 -0.02315
11/7/2016 23:46 312 -0.0204
11/7/2016 23:51 312 -0.01915
11/7/2016 23:56 312 -0.018
11/8/2016 0:01 313 -0.01895
11/8/2016 0:06 313 -0.0195
11/8/2016 0:11 313 -0.0152
11/8/2016 0:16 313 -0.0157
11/8/2016 0:21 313 -0.0177
11/8/2016 0:26 313 -0.0179
11/8/2016 0:31 313 -0.0185
11/8/2016 0:36 313 -0.0164
11/8/2016 0:41 313 -0.0145
11/8/2016 0:46 313 -0.0158
11/8/2016 0:51 313 -0.01295
11/8/2016 0:56 313 -0.0149
11/8/2016 1:01 313 -0.014
11/8/2016 1:06 313 -0.01505
11/8/2016 1:11 313 -0.01795
11/8/2016 1:16 313 -0.01375
11/8/2016 1:21 313 -0.0066
11/8/2016 1:26 313 -0.00835
11/8/2016 1:31 313 -0.00785
11/8/2016 1:36 313 -0.0082
11/8/2016 1:41 313 -0.0108
11/8/2016 1:46 313 -0.01275
11/8/2016 1:51 313 -0.01515
11/8/2016 1:56 313 -0.01505
11/8/2016 2:01 313 -0.01805
11/8/2016 2:06 313 -0.01875
11/8/2016 2:11 313 -0.01955
11/8/2016 2:16 313 -0.0201
11/8/2016 2:21 313 -0.0183
11/8/2016 2:26 313 -0.01715
11/8/2016 2:31 313 -0.0169
11/8/2016 2:36 313 -0.0139
11/8/2016 2:41 313 -0.0145
11/8/2016 2:46 313 -0.0162
11/8/2016 2:51 313 -0.01275
11/8/2016 2:56 313 -0.01285
11/8/2016 3:01 313 -0.01605
11/8/2016 3:06 313 -0.0133
11/8/2016 3:11 313 -0.00905
11/8/2016 3:16 313 -0.0149
11/8/2016 3:21 313 -0.01395
11/8/2016 3:26 313 -0.01115
11/8/2016 3:31 313 -0.0108
11/8/2016 3:36 313 -0.01015
11/8/2016 3:41 313 -0.00805
11/8/2016 3:46 313 -0.00735
11/8/2016 3:51 313 -0.00615
11/8/2016 3:56 313 -0.0055
11/8/2016 4:01 313 -0.0138
11/8/2016 4:06 313 -0.01405
11/8/2016 4:11 313 -0.01755
11/8/2016 4:16 313 -0.0181
11/8/2016 4:21 313 -0.01675
11/8/2016 4:26 313 -0.0165
11/8/2016 4:31 313 -0.01455
11/8/2016 4:36 313 -0.01425
11/8/2016 4:41 313 -0.0146
11/8/2016 4:46 313 -0.0152
11/8/2016 4:51 313 -0.0125
11/8/2016 4:56 313 -0.0117
11/8/2016 5:01 313 -0.01215
11/8/2016 5:06 313 -0.0125
11/8/2016 5:11 313 -0.0132
11/8/2016 5:16 313 -0.0126
11/8/2016 5:21 313 -0.0135
11/8/2016 5:26 313 -0.01165
11/8/2016 5:31 313 -0.00775
11/8/2016 5:36 313 -0.00695
11/8/2016 5:41 313 -0.00385
11/8/2016 5:46 313 -0.00235
11/8/2016 5:51 313 0.0028
11/8/2016 5:56 313 0.01585
11/8/2016 6:01 313 0.03635
11/8/2016 6:06 313 0.07065
11/8/2016 6:11 313 0.1311
11/8/2016 6:16 313 0.21305
11/8/2016 6:21 313 0.32055
11/8/2016 6:26 313 0.43565
11/8/2016 6:31 313 0.5715
11/8/2016 6:36 313 0.7204
11/8/2016 6:41 313 0.8756
11/8/2016 6:46 313 1.0433
11/8/2016 6:51 313 1.2124
11/8/2016 6:56 313 1.3829
11/8/2016 7:01 313 1.5636
11/8/2016 7:06 313 1.7513
11/8/2016 7:11 313 1.9341
11/8/2016 7:16 313 2.11025
11/8/2016 7:21 313 2.28195
11/8/2016 7:26 313 2.46095
11/8/2016 7:31 313 2.64895
11/8/2016 7:36 313 2.83475
11/8/2016 7:41 313 3.01725
11/8/2016 7:46 313 3.19545
11/8/2016 7:51 313 3.37045
11/8/2016 7:56 313 3.5479
11/8/2016 8:01 313 3.71555
11/8/2016 8:06 313 3.89685
11/8/2016 8:11 313 4.0722
11/8/2016 8:16 313 4.24365
11/8/2016 8:21 313 4.421
11/8/2016 8:26 313 4.6007
11/8/2016 8:31 313 4.7579
11/8/2016 8:36 313 4.9085
11/8/2016 8:41 313 5.0742
11/8/2016 8:46 313 5.2702
11/8/2016 8:51 313 5.43175
11/8/2016 8:56 313 5.5679
11/8/2016 9:01 313 5.70595
11/8/2016 9:06 313 5.8536
11/8/2016 9:11 313 6.00405
11/8/2016 9:16 313 6.14975
11/8/2016 9:21 313 6.28225
11/8/2016 9:26 313 6.3957
11/8/2016 9:31 313 6.49145
11/8/2016 9:36 313 6.61005
11/8/2016 9:41 313 6.7059
11/8/2016 9:46 313 6.803
11/8/2016 9:51 313 6.9047
11/8/2016 9:56 313 6.99005
11/8/2016 10:01 313 7.10665
11/8/2016 10:06 313 7.1775
11/8/2016 10:11 313 7.24965
11/8/2016 10:16 313 7.32285
11/8/2016 10:21 313 7.40145
11/8/2016 10:26 313 7.4465
11/8/2016 10:31 313 7.48625
11/8/2016 10:36 313 7.5403
11/8/2016 10:41 313 7.56665
11/8/2016 10:46 313 7.6129
11/8/2016 10:51 313 7.6587
11/8/2016 10:56 313 7.65805
11/8/2016 11:01 313 7.69065
11/8/2016 11:06 313 7.69305
11/8/2016 11:11 313 7.75695
11/8/2016 11:16 313 7.7813
11/8/2016 11:21 313 7.807
11/8/2016 11:26 313 7.84605
11/8/2016 11:31 313 7.86405
11/8/2016 11:36 313 7.86835
11/8/2016 11:41 313 7.71245
11/8/2016 11:46 313 7.81435
11/8/2016 11:51 313 7.78805
11/8/2016 11:56 313 7.7583
11/8/2016 12:01 313 7.70065
11/8/2016 12:06 313 7.6603
11/8/2016 12:11 313 7.622
11/8/2016 12:16 313 7.56315
11/8/2016 12:21 313 7.4049
11/8/2016 12:26 313 7.4034
11/8/2016 12:31 313 7.278
11/8/2016 12:36 313 7.3192
11/8/2016 12:41 313 7.19265
11/8/2016 12:46 313 7.4927
11/8/2016 12:51 313 7.54555
11/8/2016 12:56 313 7.69435
11/8/2016 13:01 313 6.95105
11/8/2016 13:06 313 6.26065
11/8/2016 13:11 313 6.90735
11/8/2016 13:16 313 6.4603
11/8/2016 13:21 313 5.69755
11/8/2016 13:26 313 5.30295
11/8/2016 13:31 313 5.993
11/8/2016 13:36 313 6.24425
11/8/2016 13:41 313 5.89575
11/8/2016 13:46 313 6.3803
11/8/2016 13:51 313 6.17455
11/8/2016 13:56 313 5.6555
11/8/2016 14:01 313 5.0811
11/8/2016 14:06 313 3.33805
11/8/2016 14:11 313 3.131
11/8/2016 14:16 313 3.87235
11/8/2016 14:21 313 4.3724
11/8/2016 14:26 313 4.6554
11/8/2016 14:31 313 4.7956
11/8/2016 14:36 313 3.41335
11/8/2016 14:41 313 3.11155
11/8/2016 14:46 313 3.9269
11/8/2016 14:51 313 2.8726
11/8/2016 14:56 313 2.68095
11/8/2016 15:01 313 2.98235
11/8/2016 15:06 313 3.1635
11/8/2016 15:11 313 3.09815
11/8/2016 15:16 313 2.89455
11/8/2016 15:21 313 2.7253
11/8/2016 15:26 313 2.52735
11/8/2016 15:31 313 2.30685
11/8/2016 15:36 313 1.9471
11/8/2016 15:41 313 1.76245
11/8/2016 15:46 313 1.7001
11/8/2016 15:51 313 1.509
11/8/2016 15:56 313 1.31435
11/8/2016 16:01 313 1.1337
11/8/2016 16:06 313 0.9801
11/8/2016 16:11 313 0.83105
11/8/2016 16:16 313 0.67265
11/8/2016 16:21 313 0.53225
11/8/2016 16:26 313 0.41065
11/8/2016 16:31 313 0.3211
11/8/2016 16:36 313 0.2437
11/8/2016 16:41 313 0.1663
11/8/2016 16:46 313 0.08585
11/8/2016 16:51 313 0.02745
11/8/2016 16:56 313 -0.001
11/8/2016 17:01 313 -0.0124
11/8/2016 17:06 313 -0.01965
11/8/2016 17:11 313 -0.0209
11/8/2016 17:16 313 -0.0219
11/8/2016 17:21 313 -0.02165
11/8/2016 17:26 313 -0.0221
11/8/2016 17:31 313 -0.021
11/8/2016 17:36 313 -0.02155
11/8/2016 17:41 313 -0.0211
11/8/2016 17:46 313 -0.0214
11/8/2016 17:51 313 -0.0222
11/8/2016 17:56 313 -0.0209
11/8/2016 18:01 313 -0.0217
11/8/2016 18:06 313 -0.0225
11/8/2016 18:11 313 -0.0215
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Answer

TL;DR: This looks like a timezone issue. When you convert the dates to POSIXct, the default timezone is your local timezone. But when you run date_format() inside ggplot, the dates are converted to GMT before plotting, so times are all shifted by the difference between GMT and your local timezone. To get the correct hours plotted, you can either explicitly set the desired timezone within date_format or you can explicitly set the timezone to GMT when you convert Date to POSIXct.


Before working on the ggplot code, let's look at your data. Below, I've started with your data before the conversion of Date to POSIXct:

head(original_data)
str(original_data)
            Date DOY Reference
1 11/7/2016 0:01 312  -0.01370
2 11/7/2016 0:06 312  -0.01525
3 11/7/2016 0:11 312  -0.01325
4 11/7/2016 0:16 312  -0.01235
5 11/7/2016 0:21 312  -0.01190
6 11/7/2016 0:26 312  -0.01120

'data.frame': 864 obs. of  3 variables:
$ Date     : chr  "11/7/2016 0:01" "11/7/2016 0:06" "11/7/2016 0:11" "11/7/2016 0:16" ...
$ DOY      : int  312 312 312 312 312 312 312 312 312 312 ...
$ Reference: num  -0.0137 -0.0152 -0.0132 -0.0123 -0.0119 ...

Now let's convert Date to POSIXct in two different ways: First, without setting the timezone and then with setting the timezone to GMT. Note that Date1 is in my local timezone (U.S. Pacific), while Date2 is in GMT, though the literal time strings are the same:

original_data$Date1 <- as.POSIXct(x = original_data$Date, format = "%m/%d/%Y %H:%M")
original_data$Date2 <- as.POSIXct(x = original_data$Date, format = "%m/%d/%Y %H:%M", tz="GMT")

head(original_data$Date1) 
[1] "2016-11-07 00:01:00 PST" "2016-11-07 00:06:00 PST" "2016-11-07 00:11:00 PST" "2016-11-07 00:16:00 PST"
[5] "2016-11-07 00:21:00 PST" "2016-11-07 00:26:00 PST"
head(original_data$Date2)
[1] "2016-11-07 00:01:00 GMT" "2016-11-07 00:06:00 GMT" "2016-11-07 00:11:00 GMT" "2016-11-07 00:16:00 GMT"
[5] "2016-11-07 00:21:00 GMT" "2016-11-07 00:26:00 GMT"

Here's the code for the date_format function. Note the default tz (timezone) setting is UTC, which is the same as GMT. So date_format is shifting time values from the your data's timezone to GMT:

date_format
function (format = "%Y-%m-%d", tz = "UTC") 
{
    function(x) format(x, format, tz = tz)
}

Now for ggplot: First we'll work with Date1. In the examples below, note that when we use the default date formatting, the hours are correct. However, when we use scale_x_datetime without specifying a timezone, it looks like ggplot is shifting from my local timezone (U.S. Pacific) to GMT, which is 8 hours later. However, when I specify the "America/Los_Angeles" timezone in date_format(), I get the desired hour values.

# Create plot with Date1, but without scale_x_datetime
p = ggplot(original_data, aes(Date1, Reference)) +
  facet_wrap(~ DOY, scales="free_x") + 
  xlab("Time (hours)") + 
  geom_point() +     
  ylab(expression(Radiation ~ (W ~ m^{-2}))) +
  ggtitle("Calibration Plots") + 
  theme_bw() + 
  theme(axis.title=element_text(size=12,face="bold"), 
        title = element_text(size=9, face = "bold"))

p + scale_x_datetime(date_breaks = "3 hours") + 
  ggtitle("Default date formatting") + 
  theme(axis.text.x=element_text(size=9, angle=-90, , vjust=0.5))
p + scale_x_datetime(date_breaks = "3 hours", labels=date_format("%H")) + 
  ggtitle('date_format("%H")')
p + scale_x_datetime(date_breaks = "3 hours", labels=date_format("%H", tz="America/Los_Angeles")) +
  ggtitle('date_format("%H", tz="America/Los_Angeles")')

enter image description here

On the other hand, if we use Date2, which is already set to the GMT timezone, then we don't need to specify the timezone within date_format():

# Create plot with Date2, but without scale_x_datetime
p = ggplot(original_data, aes(Date2, Reference)) +
  facet_wrap(~ DOY, scales="free_x") + 
  xlab("Time (hours)") + 
  geom_point() +     
  ylab(expression(Radiation ~ (W ~ m^{-2}))) +
  ggtitle("Calibration Plots") + 
  theme_bw() + 
  theme(axis.title=element_text(size=12,face="bold"), 
        title = element_text(size=9, face = "bold"))

p + scale_x_datetime(date_breaks = "3 hours") + 
  ggtitle("Default date formatting") + 
  theme(axis.text.x=element_text(size=9, angle=-90, , vjust=0.5))
p + scale_x_datetime(date_breaks = "3 hours", labels=date_format("%H")) + 
  ggtitle('date_format("%H")')
p + scale_x_datetime(date_breaks = "3 hours", labels=date_format("%H", tz="GMT")) +
  ggtitle('date_format("%H", tz="GMT")')

enter image description here