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automaticly add p-values to facet plot
Asked Answered
rggplot2p-value
P

1

3

I have made a facet plot below using the following command:

    ggplot(data, aes(factor(Length),logFC)),
 + geom_boxplot(fill = "grey90"),
 +  coord_cartesian(ylim=c(-5,5)) + facet_grid(X~Modification)

Is there a way to compute p-values for each boxplot and add them as geom_text above each boxplot. I want to compute a t-test and compare against y=0.

My data looks like this:

    X Length          logFC     Modification
 Daub     26    -0.7307060811           NTA
 Daub     22    -0.3325621272           NTA
 Daub     22    -2.0579390395           NTA
 Daub     25     2.7199391457           NTA
 Daub     23    -0.0009869389           NTA
 Daub     25    -0.3318842493           NTA
 ...

enter image description here

My error message:

> data <- structure(list(Experiment = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 
+                                                 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
+                                                 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
+                                                 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 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, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
+                                                 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
+                                                 2L, 2L, 2L, 2L, 2L, 2L, 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, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
+                                                 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
+                                                 3L, 3L, 3L, 3L, 3L, 
+                                                 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
+                                                 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = c("Daub", "Marie", 
+                                                                                                 "Meister"), class = "factor"), Length = c(26L, 22L, 22L, 25L, 
+                                                                                                                                           23L, 25L, 23L, 25L, 24L, 23L, 24L, 26L, 24L, 21L, 20L, 21L, 22L, 
+                                                   22L, 21L, 21L, 21L, 22L, 21L, 22L, 21L, 21L, 20L, 20L, 21L, 25L, 
+                                                                                                                                           20L, 22L, 24L, 22L, 23L, 24L, 23L, 23L, 22L, 22L, 22L, 22L, 21L, 
+                                                                                                                                           19L, 21L, 20L, 20L, 20L, 19L, 19L, 19L, 22L, 23L, 23L, 22L, 23L, 
+                                                                                                                                           22L, 20L, 21L, 24L, 24L, 24L, 25L, 24L, 21L, 20L, 23L, 23L, 20L, 
+                                                                                                                                           23L, 23L, 24L, 20L, 21L, 22L, 24L, 23L, 22L, 23L, 22L, 23L, 23L, 
+                                                                                                                                           19L, 21L, 23L, 24L, 22L, 23L, 23L, 21L, 22L, 20L, 22L, 23L, 25L, 
+                                                                                                                                           22L, 22L, 23L, 22L, 23L, 25L, 25L, 24L, 24L, 23L, 22L, 22L, 25L, 
+                                                                                                                                           23L, 24L, 23L, 23L, 22L, 22L, 25L, 23L, 22L, 25L, 21L, 19L, 21L, 
+                                                                                                                                           23L, 22L, 22L, 20L, 20L, 20L, 23L, 22L, 21L, 21L, 23L, 23L, 23L, 
+                                                                                                                                           21L, 25L, 23L, 24L, 24L, 23L, 23L, 23L, 21L, 22L, 21L, 21L, 23L, 
+                                                                                                                                           23L, 22L, 22L, 21L, 22L, 22L, 25L, 24L, 24L, 22L, 24L, 24L, 23L, 
+                                                                                                                                           22L, 21L, 22L, 23L, 20L, 22L, 23L, 24L, 25L, 24L, 25L, 22L, 23L, 
+                                                                                                                                           24L, 21L, 25L, 23L, 19L, 21L, 21L, 22L, 20L, 21L, 18L, 20L, 20L, 
+                                                                                                                                           21L, 20L, 23L, 19L, 19L, 22L, 22L, 22L, 22L, 22L, 21L, 22L, 24L, 
+                                                                                                                                           20L, 21L, 22L, 22L, 21L, 21L, 21L, 21L, 21L, 23L, 23L, 23L, 25L, 
+                                                                                                                                           25L, 25L, 23L, 24L, 24L, 24L, 24L, 24L, 24L, 25L, 25L), logFC = c(-0.7307060811, 
+                                                                                                                                                                                                             -0.3325621272, -2.0579390395, 2.7199391457, -0.0009869389, -0.3318842493, 
+                                                                                                                                                                                                             -2.1922199037, -1.8907961065, -1.9059255014, -0.2815081355, -0.2040330335, 
+                                                                                                                                                                                                             3.661469505, 0.6489955587, -0.0261245467, -1.4312409441, -1.1199604078, 
+                                                                                                                                                                                                             -1.6528592355, -2.8208936451, -0.7207549269, -1.6528592355, -1.2540377475, 
+                                                                                                                                                                                                             -2.1088724443, -2.1088724443, -1.5556550771, -1.5556550771, -0.2899601367, 
+                                                                                                                                                                                                             0.36449851, -1.7787723427, -1.5556550771, -1.5556550771, -1.5556550771, 
+                                                                                                                                                                                                             -2.1092566794, 0.0417776477, -3.0768675589, -4.2573082637, -1.5556550771, 
+                                                                                                                                                                                                             -1.8493703566, -0.7310899725, -2.8201262449, -0.7203706918, -2.1088724443, 
+                                                                                                                                                                                                             -3.5714106365, -1.5556550771, -1.2144625017, 1.6608916211, -0.3147141406, 
+                                                                                                                                                                                                             1.2344697053, 1.2303596917, 1.2138067782, 0.9409846988, 0.5270928206, 
+                                                                                                                                                                                                             -1.0435216994, -1.4320081419, -1.1644217165, -1.1478237529, -0.9941196613, 
+                                                                                                                                                                                                             0.0762668692, 1.0076747803, 0.0679302699, -0.4852244221, 0.7792467457, 
+                                                                                                                                                                                                             0.4902414285, 1.6172022872, 0.5270928206, -1.5403877099, -0.3322684844, 
+                                                                                                                                                                                                             0.0965099283, 0.8067662712, -0.3322684844, -1.2928579903, 0.6067208763, 
+                                                                                                                                                                                                             0.0247576412, -0.0291609233, -0.4737578429, 0.0743062433, 0.1126554177, 
+                                                                                                                                                                                                             -0.0156954476, 1.1069888258, -0.956482117, -0.2829742145, 0.8511530937, 
+                                                                                                                                                                                                             -0.1571780266, -1.2033199926, -1.1883052896, -0.0619556757, -0.7813018565, 
+                                                                                                                                                                                                             2.2467468049, 2.8382841074, 0.5658773933, -0.4461699001, -0.7409548873, 
+                                                                                                                                                                                                             -0.992979577, -1.0966445642, -0.8035321174, 0.4586171366, -0.2760821893, 
+                                                                                                                                                                                                             0.0585422656, 0.0328935437, 0.3858231436, -0.4374188039, 1.1166538873, 
+                                                                                                                                                                                                             -1.6539303789, 0.2027459981, -0.2193112677, -0.3939953745, -1.6726108643, 
+                                                                                                                                                                                                             1.1518720793, 2.2517568637, -0.561147283, -2.1625509666, -1.65562751, 
+                                                                                                                                                                                                             -0.9048469063, -1.0759388341, 0.4938537603, 1.8754485108, -1.5944759871, 
+                                                                                                                                                                                                             1.0688499798, 2.6559945275, -1.908097968, -1.9214219995, -2.9675169126, 
+                                                                                                                                                                                                             0.0365892303, -0.8345258687, -1.0535567925, -2.0036191122, -1.6843791204, 
+                                                                                                                                                                                                             -2.5554312825, -1.5778268888, -1.576142107, -0.9398408101, 2.4453250675, 
+                                                                                                                                                                                                             -1.5434092122, -0.794414515, -0.6200158513, 0.5556353409, -1.0772272444, 
+                                                                                                                                                                                                             -0.8720587283, -0.8082062813, -0.7353916189, 0.1072543637, 0.5658773933, 
+                                                                                                                                                                                                             0.13043531, -0.0154958912, -0.868710614, -0.1922496916, 1.0682890388, 
+                                                                                                                                                                                                             -1.673413308, -0.9581901784, -1.9575141988, -1.8973257122, 1.4967046965, 
+                                                                                                                                                                                                             -2.456068976, -1.4577030552, -4.2692094743, -1.9124787897, -1.4993411082, 
+                                                                                                                                                                                                             -0.6409837734, 0.6369441273, -0.9960964825, -5.9703084924, -1.97960268, 
+                                                                                                                                                                                                             -1.2422870608, -1.5170124157, -1.9021683731, 3.4029417731, 0.1812972171, 
+                                                                                                                                                                                                             -1.6370149729, -1.749015407, -2.1677341592, -1.4942545905, -1.1137758818, 
+                                                                                                                                                                                                             -1.2428452903, -1.3014446584, 0.0287537402, -0.8721416458, -2.4062762035, 
+                                                                                                                                                                                                             -4.0278899462, -2.2229120764, -1.5950383235, -3.6098212725, -2.5979636046, 
+                                                                                                                                                                                                             0.3631424981, 1.1377073609, 0.5151459494, 0.0640542096, -0.7715375264, 
+                                                                                                                                                                                                             -1.0361077101, -0.2462753448, -2.3058140776, -0.0847179004, -0.518970228, 
+                                                                                                                                                                                                             0.8519432911, 1.9516260022, -0.5706154628, 1.240812729, 0.336736001, 
+                                                                                                                                                                                                             2.2509464232, -0.322918086, -4.4019571741, -0.5618441487, 3.4700721641, 
+                                                                                                                                                                                                             -3.9220135953, -2.1968879291, -0.1362995026, 2.164094913, -1.0688563363, 
+                                                                                                                                                                                                             0.4302583643, 2.6411096027, -3.020513717, -1.5395519303, -2.2219591633, 
+                                                                                                                                                                                                             -3.8891956255, 0.9602784132, -0.6470571429, 1.853151793, -0.3271268741, 
+                                                                                                                                                                                                             -0.9870872828, -2.516770073, -1.2898235194, -1.7246627604, -0.61328192, 
+                                                                                                                                                                                                             -3.5457352204, -2.5068717697), Modification = structure(c(1L, 
+                                                                                                                                                                                                                                                                       1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 4L, 4L, 4L, 4L, 
+                                                                                                                                                                                                                                                                       4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 
+                                                                                                                                                                                                                                                                       5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
+                                                                                                                                                                                                                                                                       3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 
+                                                                                                                                                                                                                                                                       2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
+                                                                                                                                                                                                                                                                       1L, 1L, 1L, 1L, 1L, 1L, 1L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 
+                                                                                                                                                                                                                                                                       5L, 5L, 5L, 5L, 5L, 5L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
+                                                                                                                                                                                                                                                                       4L, 4L, 4L, 4L, 4L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
+                                                                                                                                                                                                                                                                       3L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
+                                                                                                                                                                                                                                                                       2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
+                                                                                                                                                                                                                                                                       5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 
+                                                                                                                                                                                                                                                                       4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 3L, 3L, 
+                                                                                                                                                                                                                                                                       3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 
+                                                                                                                                                                                                                                                                       2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("NTA", 
+                                                                                                                                                                                                                                                                                                                                           "t3-d", "t3-u", "t5-d", "t5-u"), class = "factor")), .Names = c("Experiment", 
+                                                                                                                                                                                                                                                                                                                                                                                                           "Length", "logFC", "Modification"), class = "data.frame", row.names = c(NA, 
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   -223L))
> library(dplyr)
> pvalues <- data %>% group_by(Experiment, Modification, Length) %>%
+ filter(n() > 1) %>%
+ summarize(p.value = (t.test(logFC, mu = 0)$p.value))
Error in t.test(logFC, mu = 0) : object 'logFC' not found
Parthenogenesis answered 25/10, 2014 at 16:6 Comment(5)
You first need to describe precisely what testing strategy you deem appropriate. – Bedivere
Could you share a reproducible example of your data using dput? If it's too large, perhaps you could share 200 randomly selected rows. – Wexford
basically a t-test where x=logFC for that particular boxplot as defined by "Modification" and "Length" and y=NULL. – Parthenogenesis
@DavidRobinson added dput for all facets. should be reproducible now. – Parthenogenesis
@Parthenogenesis I cannot reproduce your error. When I paste the contents of your above answer into an R terminal, and remove the extra + or > at the start of each line, the code works for me. All I can think of to do is make sure you have the latest version of dplyr (at least 0.3). One other possibility: could you please run the line data %>% group_by(Experiment, Modification, Length) %>% filter(n() > 1) by itself and let me know what is output? – Wexford
W
4

You can do this by summarizing the data into a table of p-values. This can be done using dplyr:

library(dplyr)
pvalues <- data %>% group_by(Experiment, Modification, Length) %>%
    filter(n() > 1) %>%
    summarize(p.value = (t.test(logFC, mu = 0)$p.value))

(The line filter(n() > 1) is to get rid of any groups of size 1, for which a p-value cannot be calculated). This produces a table that looks like:

# Experiment Modification Length   p.value
# 1       Daub          NTA     22 0.3980043
# 2       Daub          NTA     23 0.3535590
# 3       Daub          NTA     24 0.5831962
# 4       Daub          NTA     25 0.9137644
# 5       Daub          NTA     26 0.6254004
# 6       Daub         t3-d     20 0.1493108

Now you can add that text to your plot using a geom_text layer, choosing some y such as y = 3:

library(ggplot2)

ggplot(data, aes(factor(Length),logFC)) + geom_boxplot(fill = "grey90") +
    coord_cartesian(ylim=c(-5,5)) + facet_grid(Experiment~Modification) +
    geom_text(aes(y = 3, label = p.value), data = pvalues, size = 1)

You will probably have to manipulate the size (and possibly angle) of your geom_text to make the plot readable. Note also that since you are performing many tests, you should probably look at the adjusted p-values rather than the raw p-values. You can compute that column with

pvalues <- pvalues %>% mutate(p.adjusted = p.adjust(p.value, method = "bonferroni"))

The function format.pval will also come in handy, especially if some of your p-values are close to 0.

Wexford answered 25/10, 2014 at 18:52 Comment(6)
I got this error trying to read in the pvalues: Error in t.test(logFC, mu = 0) : object 'logFC' not found – Parthenogenesis
@Parthenogenesis Does your data look exactly like the dput example above? – Wexford
yes it does. I tried to copy my example above, still get the error message. – Parthenogenesis
Did you have time to check my example again? – Parthenogenesis
@Parthenogenesis I cannot reproduce your problem. Were you able to install dplyr, and were there no errors on the previous lines before the "Error in t.test..." line? If so, can you edit into your answer a full reproducible version of the code that will give this problem when run? (Note, for example, that your ggplot2 line uses X while in the dput data you posted that column is called Experiment). – Wexford
Updated the question. I had to remove the original dput due to space limitations. – Parthenogenesis

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