P-value for multiple comparisons by group - stat_compare_means()

[elisheva100]

I am trying to add p-values for my box plots, but I get an error: Computation failed in stat_compare_means(): argument is of length zero
Where my data.frame: plot.data looks like:
Group value element
1 Transcribed, 0.08620690, Exons
2 Transcribed, 0.09090909, Exons
3 NonTranscribed, 0.02631579, Exons
4 Transcribed, 0.05882353, Introns
5 NonTranscribed, 0.04458599, Introns
6 NonTranscribed, 0.06716418, Introns
And my function is:
makeBoxPlot <- function(plot.data) { p <- ggplot(plot.data, aes(x = element, y = value, fill = Group)) stat_compare_means(aes(group = Group), paired = TRUE, label = "p.signif") }
I dont get any p-values bacause of the above error and I have no idea why I get this error, this function used to work before.

[giuliagrisot]

I have a similar problem from today after updating the ggpubr package, significance labels (*** etc) that used to be between columns by group disappeared the following,

ggbarplot(paired_dataset, "Text", "IA_FIRST_FIXATION_DURATION", fill = "Modified", add = "mean_se", add.params = list(group = "Modified"), position = position_dodge(0.8))+ stat_compare_means(method = "t.test", aes(group = Modified), label = "p.signif", label.y = 320, na.rm = TRUE) + labs(x = "Passage number", y = "First fixation duration", caption = "* = p value < 0.5; **** = p value < 0.0001") + scale_fill_manual(values=c("#CCCCCC","#FFFFFF")) + theme_minimal()

and I get these errors:

Removed 67697 rows containing non-finite values (stat_summary).
Removed 67697 rows containing non-finite values (stat_signif).
Computation failed in stat_signif(): missing value where TRUE/FALSE needed

any help would really be appreciated.

[sbbmu]

I have the same problem too. Using the standard data.

`library(ggpubr)
p <- ggboxplot(ToothGrowth, x = "supp", y = "len",
color = "supp", palette = "jco",
add = "jitter",
facet.by = "dose", short.panel.labs = FALSE)

p + stat_compare_means(method = "t.test", label = "p.format")`

I got these errors and no p-values show up.

Warning messages: 1: Computation failed in 'stat_compare_means()': argument is of length zero 2: Computation failed in 'stat_compare_means()': argument is of length zero 3: Computation failed in 'stat_compare_means()': argument is of length zero

[kassambara]

fixed now, thanks

[benjamin942]

I am a beginner in R. The bug is fixed now, thanks but what should i do to use stat_compare_means now ? update ggpubr package ? It doesn't work. thank you

[kassambara]

Kindly install the latest developmental version of ggpubr as follow:

if(!require(devtools)) install.packages("devtools")
devtools::install_github("kassambara/ggpubr")

Let me know if it works on your computer, so that we can close this issue

[benjamin942]

after install the last version from your link, the answer is the same

Warning messages:
1: Computation failed in stat_compare_means():
argument is of length zero
2: Computation failed in stat_compare_means():
argument is of length zero
3: Computation failed in stat_compare_means():
argument is of length zero

I try with ToothGrowth datas

library(ggpubr)
p <- ggboxplot(ToothGrowth, x = "supp", y = "len",
color = "supp", palette = "jco",
add = "jitter",
facet.by = "dose", short.panel.labs = FALSE)

p + stat_compare_means(method = "t.test", label = "p.format")

thank you for your help

[kassambara]

Please, make sure you have re-started R.

Please, provide the output of the R code devtools::session_info().

When posting your session info, insert the content inside

, to make it more readable on GitHub.

Thanks

[benjamin942]

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : l'espace de noms ‘processx’ 3.1.0 est en train de charger, mais >= 3.2.0 est requis

[kassambara]

This is strange, try to install process R package 3.2.0

install.packages("processx")

[benjamin942]

After process R installation

`- Session info -------------------------------------------------------------------------------------
setting value
version R version 3.4.2 (2017-09-28)
os Windows >= 8 x64
system x86_64, mingw32
ui RStudio
language (EN)
collate French_France.1252
ctype French_France.1252
tz Europe/Paris
date 2018-11-13

• Packages -----------------------------------------------------------------------------------------
  ! package * version date lib source
  assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.4.4)
  backports 1.1.2 2017-12-13 [1] CRAN (R 3.4.3)
  base64enc 0.1-3 2015-07-28 [1] CRAN (R 3.4.1)
  bindr 0.1.1 2018-03-13 [1] CRAN (R 3.4.4)
  bindrcpp 0.2.2 2018-03-29 [1] CRAN (R 3.4.4)
  boot 1.3-20 2017-08-06 [2] CRAN (R 3.4.2)
  callr 3.0.0 2018-08-24 [1] CRAN (R 3.4.4)
  cellranger 1.1.0 2016-07-27 [1] CRAN (R 3.4.2)
  cli 1.0.1 2018-09-25 [1] CRAN (R 3.4.4)
  colorspace 1.3-2 2016-12-14 [1] CRAN (R 3.4.4)
  crayon 1.3.4 2017-09-16 [1] CRAN (R 3.4.4)
  curl 3.2 2018-03-28 [1] CRAN (R 3.4.4)
  desc 1.2.0 2018-05-01 [1] CRAN (R 3.4.4)
  devtools 2.0.1 2018-10-26 [1] CRAN (R 3.4.4)
  digest 0.6.18 2018-10-10 [1] CRAN (R 3.4.4)
  dplyr 0.7.8 2018-11-10 [1] CRAN (R 3.4.4)
  fs 1.2.6 2018-08-23 [1] CRAN (R 3.4.4)
  ggplot2 * 3.1.0 2018-10-25 [1] CRAN (R 3.4.4)
  ggpubr * 0.1.9 2018-11-11 [1] CRAN (R 3.4.2)
  glue 1.3.0 2018-07-17 [1] CRAN (R 3.4.4)
  gtable 0.2.0 2016-02-26 [1] CRAN (R 3.4.4)
  labeling 0.3 2014-08-23 [1] CRAN (R 3.4.1)
  lazyeval 0.2.1 2017-10-29 [1] CRAN (R 3.4.4)
  magrittr * 1.5 2014-11-22 [1] CRAN (R 3.4.4)
  memoise 1.1.0 2017-04-21 [1] CRAN (R 3.4.4)
  munsell 0.5.0 2018-06-12 [1] CRAN (R 3.4.4)
  pastecs * 1.3.21 2018-03-15 [1] CRAN (R 3.4.4)
  pillar 1.3.0 2018-07-14 [1] CRAN (R 3.4.4)
  pkgbuild 1.0.2 2018-10-16 [1] CRAN (R 3.4.4)
  pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.4.4)
  pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.4.4)
  plyr 1.8.4 2016-06-08 [1] CRAN (R 3.4.4)
  prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.4.4)
  processx 3.2.0 2018-08-16 [1] CRAN (R 3.4.4)
  ps 1.2.1 2018-11-06 [1] CRAN (R 3.4.4)
  purrr 0.2.5 2018-05-29 [1] CRAN (R 3.4.4)
  V R6 2.2.2 2018-10-04 [1] CRAN (R 3.4.4)
  Rcpp 1.0.0 2018-11-07 [1] CRAN (R 3.4.4)
  readxl * 1.0.0 2017-04-18 [1] CRAN (R 3.4.2)
  remotes 2.0.2 2018-10-30 [1] CRAN (R 3.4.4)
  rlang 0.3.0.1 2018-10-25 [1] CRAN (R 3.4.4)
  rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.4.4)
  rstudioapi 0.7 2017-09-07 [1] CRAN (R 3.4.4)
  R scales 0.5.0 [1]
  sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.4.4)
  testthat 2.0.0 2017-12-13 [1] CRAN (R 3.4.4)
  tibble 1.4.2 2018-01-22 [1] CRAN (R 3.4.4)
  tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.4.4)
  usethis 1.4.0 2018-08-14 [1] CRAN (R 3.4.4)
  withr 2.1.2 2018-03-15 [1] CRAN (R 3.4.4)
  yaml 2.1.19 2018-05-01 [1] CRAN (R 3.4.4)

[1] C:/Users/benjd/OneDrive/Documents/R/win-library/3.4
[2] C:/Program Files/R/R-3.4.2/library

V -- Loaded and on-disk version mismatch.
R -- Package was removed from disk.`

but stat_compare_means shows
Warning message: Computation failed in stat_compare_means(): argument is of length zero

[kassambara]

I can see that you have the CRAN version of ggpubr. You need to install the latest developmental version from GitHub as follow:

if(!require(devtools)) install.packages("devtools")
devtools::install_github("kassambara/ggpubr")

[benjamin942]

It works!!! great. thank you

[giuliagrisot]

the development version install resolved that for me too. thanks

[kassambara]

thank you!!