Add error bars in box plots

[j3ypi]

I'm not quiet sure whether I don't understand the syntax or it's not implemented yet, but how do I add an errorbar to a box plot with ggpubr?

Lets say we have the same toy data all over again.

library(tidyverse)
library(ggpubr)
df <- tibble(
  iq = rnorm(100, 100, 15),
  condition = rep(c("A", "B"), each = 50),
  time = rep(c("t1", "t2", "t1", "t2"), each = 25)
)

What I like to have is something like this:

ggplot(df, aes(x = time, y = iq)) + 
  stat_boxplot(geom = "errorbar", width = 0.4)+
  geom_boxplot() 

But I haven't been able to implement the exact same mechanism with ggpubr. I tried

ggboxplot(df, 
      x = "time", 
      y = "iq",
      add = "mean_se", 
      error.plot = "errorbar")

but it appears that this function returns the errorbar of the mean and not the limits I want to border the box plots with.

[kassambara]

stat_boxplot() adds a specific errorbar to the box plot using median +/- 1.5*IQR.

In ggpubr, you have the generic option add = median_iqr, which is a non parametric alternative of mean_sd.

I think that, we need a new argument in ggboxplot(), for example show.errorbar or boxplot.errorbar.

[j3ypi]

I agree. In addition, median_iqr doens't work the same way as the example with ggplot. The errorbars aren't at the limits of the box plots and you'll see a vertical line crossing the boxplot, probably because the errorbar is added after the call of geom_boxplot() internally.

You can observe the same behavior, if you exchange the order of those two function calls like this

ggplot(df, aes(x = time, y = iq)) + 
  geom_boxplot() +
  stat_boxplot(geom = "errorbar", width = 0.4)

Or isn't this the code you had in mind with median_iqr?

ggboxplot(df, 
      x = "time", 
      y = "iq",
      add = "median_iqr", 
      error.plot = "errorbar")

[j3ypi]

I took a quick look at the ggboxplot() function. You have a lot of helper functions and checking going on in the background and I haven't checked if it works like this, but it should be as easy as adding something like

 p <- ggplot(data, aes_string(x, y))

 if (show.errobar) {
    p <- p + 
      stat_boxplot(geom = "errorbar", width = 0.4)
  } 

  p <- p + geom_exec(geom_boxplot, data = data,
                     color = color, fill = fill, linetype = linetype,
                     size = size, width = width, notch = notch,
                     position = position_dodge(0.8), size = size,...)

in line 198. In addition adding the boolean argument show.errobar to ggboxplot(), .opts and ggboxplot_core().

I never checked an unfamiliar package before, so I'll need some time to create a pull request (assuming this works), if you won't implement it yourself first anyways.

[kassambara]

New arguments added: bxp.errorbar and bxp.errorbar.width . The following R code should works:

library(ggpubr)
df <- tibble(
  iq = rnorm(100, 100, 15),
  condition = rep(c("A", "B"), each = 50),
  time = rep(c("t1", "t2", "t1", "t2"), each = 25)
)
  
  ggboxplot(df, 
            x = "time", 
            y = "iq",
            bxp.errorbar = TRUE)

[j3ypi]

Man you work fast. Keep up the good work!

[kassambara]

Thank you for the feedback, highly appreciated!

[RoseString]

@kassambara This is a great functionality. I noticed that the default color for the error bar is black. Do you know if it can be changed to the one I set in "color="? Thank you very much!

[Keniajin]

Thanks, @kassambara for the update, when I try

ggboxplot(df, 
          x = "time", 
          y = "iq",
          fill="condition",
          bxp.errorbar = TRUE)

The error bar doesn't appear on each of the fill boxplots

[jaydoc]

Hi there

Has this been fixed? When using a variable as the "fill" or "color" condition, the bxp.errorbar function seems tobe calculated for the entire dataset grouped by the "x" variable, rather than the subgroups created by the "fill" condition.

Thanks, @kassambara for the update, when I try

ggboxplot(df, 
          x = "time", 
          y = "iq",
          fill="condition",
          bxp.errorbar = TRUE)

The error bar doesn't appear on each of the fill boxplots

[kassambara]

@RoseString, @Keniajin, @jaydoc: fixed now, thanks!

[jaydoc]

That was literally the quickest a developer has fixed an issue in my experience! Thanks a bunch.