Why error bar doesn't show up in ggpubr::ggbarplot even after adding add='mean_se'

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I have the following data frame:

library(tidyverse)
df <- structure(list(genes = c(
  "Ccl2", "Bar", "Wnt5a", "Ccl2", "Ccl2",
  "Bar", "Ccl2", "Wnt5a", "Wnt5a", "Bar", "Ccl2", "Bar", "Wnt5a",
  "Bar", "Ccl2", "Ccl2", "Ccl2", "Bar", "Ccl2", "Wnt5a", "Ccl2",
  "Bar", "Bar", "Wnt5a", "Bar", "Ccl2", "Ccl2", "Ccl2", "Bar",
  "Bar", "Ccl2", "Wnt5a", "Ccl2", "Wnt5a", "Bar", "Bar", "Bar",
  "Ccl2", "Bar", "Bar", "Wnt5a", "Wnt5a", "Wnt5a", "Wnt5a", "Ccl2",
  "Wnt5a", "Bar", "Bar", "Bar", "Bar", "Ccl2"
), gexp = c(
  0,
  2, 0, 0, 0, 3, 0, 0, 0, 11, 0, 1, 0, 6, 0, 0, 0, 3, 0, 0, 0,
  2, 0, 0, 7, 0, 0, 0, 13, 2, 0, 0, 0, 0, 4, 2, 10, 0, 2, 3, 0,
  0, 0, 0, 0, 0, 6, 0, 1, 3, 11
), Treat = c(
  "Non_Treat", "Non_Treat",
  "Foo", "Foo", "Non_Treat", "Foo", "Saline", "Non_Treat", "Foo",
  "Saline", "Foo", "Foo", "Foo", "Foo", "Non_Treat", "Foo",
  "Foo", "Saline", "Non_Treat", "Foo", "Foo", "Saline", "Non_Treat",
  "Foo", "Foo", "Foo", "Foo", "Non_Treat", "Foo", "Foo",
  "Foo", "Foo", "Saline", "Non_Treat", "Non_Treat", "Non_Treat",
  "Foo", "Foo", "Non_Treat", "Saline", "Foo", "Foo", "Non_Treat",
  "Foo", "Foo", "Foo", "Non_Treat", "Non_Treat", "Non_Treat",
  "Non_Treat", "Foo"
), partition = c(
  1, 1, 1, 1, 1, 1, 1, 1, 1,
  1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
  1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
), cell_name = c(
  "SaP", "SaP", "SaP", "SaP", "SaP", "SaP", "SaP",
  "SaP", "SaP", "SaP", "SaP", "SaP", "SaP", "SaP", "SaP", "SaP",
  "SaP", "SaP", "SaP", "SaP", "SaP", "SaP", "SaP", "SaP", "SaP",
  "SaP", "SaP", "SaP", "SaP", "SaP", "SaP", "SaP", "SaP", "SaP",
  "SaP", "SaP", "SaP", "SaP", "SaP", "SaP", "SaP", "SaP", "SaP",
  "SaP", "SaP", "SaP", "SaP", "SaP", "SaP", "SaP", "SaP"
), Qux_status = c(
  "Qux-",
  "Qux-", "Qux-", "Qux-", "Qux-", "Qux-", "Qux-", "Qux-",
  "Qux-", "Qux-", "Qux+", "Qux-", "Qux-", "Qux-", "Qux+",
  "Qux-", "Qux-", "Qux-", "Qux-", "Qux-", "Qux-", "Qux-",
  "Qux-", "Qux-", "Qux-", "Qux+", "Qux+", "Qux-", "Qux-",
  "Qux-", "Qux-", "Qux-", "Qux-", "Qux-", "Qux-", "Qux-",
  "Qux-", "Qux-", "Qux-", "Qux-", "Qux-", "Qux-", "Qux-",
  "Qux-", "Qux+", "Qux-", "Qux+", "Qux-", "Qux-", "Qux-",
  "Qux-"
), sname = structure(c(
  4L, 4L, 6L, 6L, 4L, 6L, 5L, 4L,
  6L, 5L, 3L, 6L, 6L, 6L, 1L, 6L, 6L, 5L, 4L, 6L, 6L, 5L, 4L, 6L,
  6L, 3L, 3L, 4L, 6L, 6L, 6L, 6L, 5L, 4L, 4L, 4L, 6L, 6L, 4L, 5L,
  6L, 6L, 4L, 6L, 3L, 6L, 1L, 4L, 4L, 4L, 6L
), .Label = c(
  "Qux+.Non_Treat",
  "Qux+.Saline", "Qux+.Foo", "Qux-.Non_Treat", "Qux-.Saline",
  "Qux-.Foo"
), class = "factor")), row.names = c(NA, -51L), class = c(
  "tbl_df",
  "tbl", "data.frame"
))

I'm using ggpubr::ggbarplot to make the barpolot with error bar. With this code

ggpubr::ggbarplot(df, x = "sname", y = "gexp", add = "mean_se")

I expect the error bar to show up. But it didn't

enter image description here And it gave me this message:

Warning message:
Computation failed in `stat_summary()`:
object 'mean_se_' of mode 'function' was not found 

How can I resolve the problem?

1 Answers

I think this should not happen, but the simple fix is to load the package ggpubr first library(ggpubr). I do not know why but it works on my machine.

library(ggpubr)
ggbarplot(df, x = "sname", y = "gexp", add = "mean_se")

enter image description here

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