Solving the Mysterious Case of “add_xy_position in rstatix doesn’t work for two-way ANOVA | tukey_hsd(): Error in `group_by()`”

Are you tired of encountering the frustrating error “add_xy_position in rstatix doesn’t work for two-way ANOVA | tukey_hsd(): Error in `group_by()`” while trying to visualize your two-way ANOVA results in R? You’re not alone! In this article, we’ll dive into the root cause of this issue and provide a step-by-step guide to overcome it, ensuring you can elegantly display your Tukey’s HSD test results.

What’s the Problem?

The `rstatix` package in R provides an efficient way to perform various statistical tests, including two-way ANOVA. However, when attempting to add xy-positioning labels to the plot using `add_xy_position()`, you might encounter the following error:

Error in `group_by()`:
! Must group by variables found in `.data`.
 Column `groups` is not found.
Run `rlang::last_error()` to see where the error occurred.

This error occurs because the `group_by()` function in `dplyr` (which is used internally by `rstatix`) is unable to find the `groups` column in the data.

Understanding the `tukey_hsd()` Function

The `tukey_hsd()` function in `rstatix` is used to perform Tukey’s Honestly Significant Difference (HSD) test, a post-hoc analysis technique for comparing means between groups. The function takes a formula as input, specifying the response variable and the grouping factors.

For example, consider a two-way ANOVA model with `response` as the response variable and `factorA` and `factorB` as the grouping factors:

library(rstatix)

anova_result <- anova_test(response ~ factorA * factorB, data = my_data)
tukey_hsd(anova_result, conf.level = 0.95)

This would perform the Tukey’s HSD test for the interaction between `factorA` and `factorB`.

The `add_xy_position()` Function

The `add_xy_position()` function is used to add xy-positioning labels to a plot, allowing you to easily identify the groups being compared. However, in the context of two-way ANOVA, `add_xy_position()` requires a bit more tweaking to work correctly.

Solution: A Step-by-Step Guide

To overcome the error and successfully add xy-positioning labels to your plot, follow these steps:

1. Load the necessary libraries:

   library(rstatix)
   library(ggplot2)
   library(dplyr)
   

2. Perform the two-way ANOVA using `anova_test()`:

   anova_result <- anova_test(response ~ factorA * factorB, data = my_data)
   

3. Extract the Tukey’s HSD test results using `tukey_hsd()`:

   tukey_result <- tukey_hsd(anova_result, conf.level = 0.95)
   

4. Convert the `tukey_result` object to a dataframe:

   tukey_df <- as.data.frame(tukey_result)
   

5. Merge the original data with the Tukey’s HSD test results:

   merged_data <- left_join(my_data, tukey_df, by = c("factorA", "factorB"))
   

6. Use `ggplot2` to create a plot with the merged data:

   library(ggplot2)
   
   p <- ggplot(merged_data, aes(x = factorA, y = response, color = factorB)) +
     geom_point() +
     geom_line(aes(group = interaction(factorA, factorB))) +
     theme_classic()
   

7. Finally, add xy-positioning labels using `add_xy_position()`:

   p + add_xy_position("groups")
   

Voilà! You should now have a beautiful plot with xy-positioning labels, correctly displaying the Tukey’s HSD test results for your two-way ANOVA model.

Troubleshooting Tips

If you still encounter issues, ensure that:

• your data is properly structured, with the response variable and grouping factors correctly specified;

• you’ve loaded the necessary libraries (rstatix, ggplot2, and dplyr);

• you’ve correctly merged the original data with the Tukey’s HSD test results;

• you’ve specified the correct aesthetics in the `ggplot()` function.

Conclusion

In this article, we’ve delved into the mysterious case of “add_xy_position in rstatix doesn’t work for two-way ANOVA | tukey_hsd(): Error in `group_by()`.” By following the step-by-step guide, you should now be able to elegantly visualize your Tukey’s HSD test results for two-way ANOVA models in R. Remember to double-check your data structure, library loading, and plot aesthetics to ensure a smooth experience.

Package	Function	Description
rstatix	anova_test()	Performs two-way ANOVA
rstatix	tukey_hsd()	Performs Tukey’s HSD test
ggplot2	ggplot()	Creates a plot
rstatix	add_xy_position()	Adds xy-positioning labels to a plot

Happy plotting!

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