Error while trying to save ggplot in loop with faceted variable

[Chandra]

I'm running into an error while trying to save multiple plots in a loop. I get the following error: Error: Faceting variables must have at least one value.
If I run the ggplot line outside of the for loop, I don't get an error.  Just running the for loop by itself seems fine but when I run the print section, I get the error.

Here is my code:

library(ggplot2)
SampleLists <- unique(Mydf$Site)
plot_list = list()
for (i in SampleLists) {
  p = ggplot(subset(Mydf, Site == SampleLists[i]), aes(x = Time, y = Protein)) + stat_summary(fun.data = "mean_se", size = 0.75) + geom_line()+ facet_wrap(~Sample) + ggtitle(as.character(SampleLists[i]))
  plot_list[[i]] = p
 
}

pdf("plots.pdf")
for (i in SampleLists) {
  print(plot_list[[i]])
}
dev.off()

Thanks in advance,
Chandra



dput(Mydf)
structure(list(Sample = structure(c(19L, 19L, 19L, 1L, 1L, 1L,
20L, 20L, 20L, 2L, 2L, 2L, 21L, 21L, 21L, 3L, 3L, 3L, 22L, 22L,
22L, 4L, 4L, 4L, 23L, 23L, 23L, 24L, 24L, 24L, 6L, 6L, 6L, 5L,
5L, 5L, 25L, 25L, 25L, 7L, 7L, 7L, 26L, 26L, 26L, 8L, 8L, 8L,
27L, 27L, 27L, 9L, 9L, 9L, 10L, 10L, 10L, 28L, 28L, 28L, 29L,
29L, 29L, 11L, 11L, 11L, 12L, 12L, 12L, 31L, 31L, 31L, 13L, 13L,
13L, 32L, 32L, 32L, 33L, 33L, 33L, 14L, 14L, 14L, 15L, 15L, 15L,
16L, 16L, 16L, 17L, 17L, 17L, 18L, 18L, 18L, 19L, 19L, 19L, 1L,
1L, 1L, 20L, 20L, 20L, 2L, 2L, 2L, 21L, 21L, 21L, 3L, 3L, 3L,
22L, 22L, 22L, 4L, 4L, 4L, 23L, 23L, 23L, 24L, 24L, 24L, 6L,
6L, 6L, 5L, 5L, 5L, 25L, 25L, 25L, 7L, 7L, 7L, 26L, 26L, 26L,
8L, 8L, 8L, 27L, 27L, 27L, 9L, 9L, 9L, 10L, 10L, 10L, 28L, 28L,
28L, 29L, 29L, 29L, 11L, 11L, 11L, 30L, 30L, 30L, 12L, 12L, 12L,
31L, 31L, 31L, 13L, 13L, 13L, 32L, 32L, 32L, 33L, 33L, 33L, 14L,
14L, 14L, 15L, 15L, 15L, 16L, 16L, 16L, 17L, 17L, 17L, 19L, 19L,
19L, 1L, 1L, 1L, 20L, 20L, 20L, 2L, 2L, 2L, 21L, 21L, 21L, 3L,
3L, 3L, 22L, 22L, 22L, 4L, 4L, 4L, 23L, 23L, 23L, 24L, 24L, 24L,
6L, 6L, 6L, 5L, 5L, 5L, 25L, 25L, 25L, 7L, 7L, 7L, 26L, 26L,
26L, 8L, 8L, 8L, 27L, 27L, 27L, 9L, 9L, 9L, 10L, 10L, 10L, 28L,
28L, 28L, 29L, 29L, 29L, 11L, 11L, 11L, 30L, 30L, 30L, 12L, 12L,
12L, 31L, 31L, 31L, 13L, 13L, 13L, 32L, 32L, 32L, 33L, 33L, 33L,
14L, 14L, 14L, 15L, 15L, 15L, 16L, 16L, 16L, 17L, 17L, 17L), .Label = c("W0076",
"W0077", "W0078", "W0079", "W0080", "W0081", "W0082", "W0083",
"W0084", "W0085", "W0113", "W0114", "W0115", "W0116", "W0117",
"W0118", "W0119", "W0120", "W0419", "W0420", "W0421", "W0422",
"W0423", "W0424", "W0425", "W0426", "W0427", "W0475", "W0476",
"W0477", "W0478", "W0479", "W0480"), class = "factor"), Time = c(0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 24L,
24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L,
24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L,
24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L,
24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L,
24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L,
24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L,
24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L,
24L, 24L, 24L, 24L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L), Protein = c(33025.08787, 32621.05272, 33109.26186,
92823.91351, 99658.65946, 88215.63784, 126607.5691, 126062.4228,
120688.8374, 88465.42775, 85641.56069, 85586.19075, 31044.23049,
29184.06171, 28558.21053, 78722.31319, 76932.82967, 76880.1978,
123940.6471, 126999.4874, 121203.7899, 47333.75932, 46879.16271,
48145.53898, 29838.50758, 29384.95644, 28786.26894, 72208.38614,
71402.23267, 71449.65347, 66585.06926, 65631.31602, 64594.62771,
118007.5143, 116091.7143, 116160.1357, 254667.6327, 255058.6122,
253494.6939, 85345.35374, 82999.47619, 84758.88435, 51222.43983,
51540.41494, 47406.73859, 33860.13002, 34427.91013, 35014.00574,
64349.17269, 62925.78715, 61233.11245, 60682.78879, 60847.94397,
59857.01293, 30588.24766, 30856.81776, 30163.01168, 80698.48864,
81188.32386, 82113.56818, 87193.33129, 84019.92025, 83197.18405,
83732.26857, 82309.10286, 82528.05143, 68003.51464, 61791.19247,
60829.28452, 1574720.333, 1577115.083, 1532413.083, 97710.7713,
94832.77578, 90107.70852, 90790.76667, 90790.76667, 93345.16667,
168899.9043, 160736.9304, 158654.5391, 188730.6118, 193914.5412,
195717.6471, 200694.6147, 191115.6147, 191994.422, 53235.80567,
51257.95547, 51529.4251, 56887.58271, 55555.16541, 53934.65789,
55698.1877, 54923.1877, 54334.1877, 32969.95662, 33198.52278,
33489.42516, 50966.30868, 50196.2926, 50843.10611, 35986.85912,
36584.16397, 36739.02079, 41650.47545, 41798.98708, 41353.4522,
44110.35714, 44247.2, 43864.04, 107545.2778, 108942.2153, 109806.9861,
56843.98201, 56878.43885, 56981.80935, 38194.61391, 38470.26859,
38516.21103, 28470.80364, 28296.64, 27983.14545, 72706.66667,
73561.13146, 73965.87793, 135462.9492, 143174.8559, 133839.3898,
93960.11243, 94583.59763, 94016.7929, 45243.45697, 44589.69733,
45470.85163, 270012.807, 273709.9649, 276230.7544, 55948.10432,
56878.43885, 55948.10432, 61637.91051, 61600.63813, 61675.18288,
155484.3469, 155875.3265, 155973.0714, 52823.27148, 53744.9622,
60953.90034, 50893.1877, 50645.1877, 50459.1877, 54846.09689,
54713.51557, 55840.45675, 46137.38922, 46080.02994, 46051.3503,
61831.132, 61907.764, 61907.764, 45646.33626, 45366.24854, 45702.3538,
70558.90265, 70092.66814, 69838.35841, 25046.01127, 25169.41224,
24984.31079, 36407.18476, 36584.16397, 36340.81755, 39964.90617,
39491.86914, 39822.99506, 32393.51308, 32297.14487, 32894.62777,
49987.41613, 50141.91613, 49894.71613, 42265.14402, 42941.9212,
42941.9212, 64637.53036, 64249.7166, 64210.93522, 337041.3404,
341728.9362, 338671.8085, 67624.84977, 66455.58216, 66905.30047,
71242.26415, 71603.73585, 71242.26415, 983901.0667, 967297.4667,
983901.0667, 91310.81988, 95237.61491, 95297.1118, 64297.54545,
65386.06818, 64994.2, 134532.1509, 135435.8302, 135345.4623,
146531.47, 148830.43, 148159.9, 62908.0249, 69466.26141, 63504.22822,
85282.50595, 84199.16667, 86479.88095, 39143.80654, 39326.51226,
39874.62943, 63959.22174, 63709.33478, 64500.64348, 50018.15615,
50622.81063, 51322.93688, 113316.944, 112703.888, 114619.688,
29633.09205, 29813.44979, 30154.12552, 46884.37582, 46133.0817,
47072.19935, 49189.0034, 50427.10544, 51306.80952, 77574.77222,
80022.73889, 78160.15556, 61443.09524, 62106.57576, 62562.71861,
48613.13201, 48107.31023, 47569.87459, 115727.3403, 105150.5278,
105416.6111, 22594.25, 22958.00949, 22639.71994, 21920.10292,
22273.24578, 22420.38863, 56378.24219, 57313.69141, 55854.39063,
61409.656, 60911.548, 61869.448, 44043.16975, 43924.91049, 43777.08642,
64440.04525, 63529.82353, 65480.29864, 44031.73476, 44031.73476,
44820.25, 91342.69375, 97569.04375, 95174.29375, 54479.3, 54331.93077,
55142.46154, 47511.70684, 47948.5342, 51630.36482, 40513.02192,
39988.14521, 39751.95068, 39758.43514, 42010.79459, 41260.00811
), Site = structure(c(3L, 3L, 3L, 1L, 1L, 1L, 13L, 13L, 13L,
4L, 4L, 4L, 14L, 14L, 14L, 15L, 15L, 15L, 11L, 11L, 11L, 9L,
9L, 9L, 8L, 8L, 8L, 9L, 9L, 9L, 10L, 10L, 10L, 12L, 12L, 12L,
12L, 12L, 12L, 13L, 13L, 13L, 4L, 4L, 4L, 11L, 11L, 11L, 5L,
5L, 5L, 3L, 3L, 3L, 8L, 8L, 8L, 7L, 7L, 7L, 4L, 4L, 4L, 13L,
13L, 13L, 6L, 6L, 6L, 13L, 13L, 13L, 11L, 11L, 11L, 3L, 3L, 3L,
8L, 8L, 8L, 12L, 12L, 12L, 8L, 8L, 8L, 3L, 3L, 3L, 2L, 2L, 2L,
11L, 11L, 11L, 3L, 3L, 3L, 1L, 1L, 1L, 13L, 13L, 13L, 4L, 4L,
4L, 14L, 14L, 14L, 15L, 15L, 15L, 11L, 11L, 11L, 9L, 9L, 9L,
8L, 8L, 8L, 9L, 9L, 9L, 10L, 10L, 10L, 12L, 12L, 12L, 12L, 12L,
12L, 13L, 13L, 13L, 4L, 4L, 4L, 11L, 11L, 11L, 5L, 5L, 5L, 3L,
3L, 3L, 8L, 8L, 8L, 7L, 7L, 7L, 4L, 4L, 4L, 13L, 13L, 13L, 12L,
12L, 12L, 6L, 6L, 6L, 13L, 13L, 13L, 11L, 11L, 11L, 3L, 3L, 3L,
8L, 8L, 8L, 12L, 12L, 12L, 8L, 8L, 8L, 3L, 3L, 3L, 2L, 2L, 2L,
3L, 3L, 3L, 1L, 1L, 1L, 13L, 13L, 13L, 4L, 4L, 4L, 14L, 14L,
14L, 15L, 15L, 15L, 11L, 11L, 11L, 9L, 9L, 9L, 8L, 8L, 8L, 9L,
9L, 9L, 10L, 10L, 10L, 12L, 12L, 12L, 12L, 12L, 12L, 13L, 13L,
13L, 4L, 4L, 4L, 11L, 11L, 11L, 5L, 5L, 5L, 3L, 3L, 3L, 8L, 8L,
8L, 7L, 7L, 7L, 4L, 4L, 4L, 13L, 13L, 13L, 12L, 12L, 12L, 6L,
6L, 6L, 13L, 13L, 13L, 11L, 11L, 11L, 3L, 3L, 3L, 8L, 8L, 8L,
12L, 12L, 12L, 8L, 8L, 8L, 3L, 3L, 3L, 2L, 2L, 2L), .Label = c("ARC",
"Bol", "CDC", "DEB", "Fra", "Fra_cor", "Fra2", "HIG", "LDS",
"Leb", "MUS", "NAR", "SAN", "Tur", "Uru"), class = "factor")), .Names = c("Sample",
"Time", "Protein", "Site"), class = "data.frame", row.names = c(NA,
-288L))

[Pedro Aphalo]

You are using a factor for indexing the list which is not usually a good idea. 

To start with replace `SampleLists <- unique(Mydf$Site)` with `SampleLists <- levels(Mydf$Site)`.

This does not look to me necessarily as a ggplot2 problem, so do first debug the loops, and provide a simple and reproducible example of the problem using simple data if it persists and it is related to ggplot2.

Be aware that error messages like you describe are only triggered on printing even if they have to do with problems in the plotted data. Do all individual plots trigger the error or only some?