The dot-dot notation (`..p.adj..`) was deprecated in ggplot2 3.4.0.

[github-wow]

exp_len <- repExplore(my_data$data, .method = "len", .col = "aa") vis(exp_len, .by = "parameter", .meta = my_data$meta)
returned:

Warning message:
The dot-dot notation (`..p.adj..`) was deprecated in ggplot2 3.4.0.
ℹ Please use `after_stat(p.adj)` instead.
ℹ The deprecated feature was likely used in the immunarch package.
  Please report the issue at <https://github.com/immunomind/immunarch/issues>.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.

[Alexander230]

Hi, @github-wow!

Please try to install the development version of Immunarch like described here https://immunarch.com/#latest-pre-release-on-github, I've added the fix to avoid this warning.

Best regards, Aleksandr

[github-wow]

That one disappeared.

Now when I do the following for my_var with 3 levels:

repExplore(my_data$data, "len") %>% vis(.by = "my_var", .meta = my_data$meta)

I see that the error bars in each CDR3 length bin are grouped within the width of the middle group of my_var rather than located in the middle of the width of each group. It is visualized on the right histogram on p. 21 in: https://www.antibodysociety.org/wordpress/wp-content/uploads/2021/10/Nazarov-AIRR-webinar_final.pdf

Also, I guess it would be ok to mention it here (otherwise I can open another case). When I do:

repExplore(my_data$data, "clones") %>% vis(.by = "my_var", .meta = my_data$meta) or repDiversity(my_data, "chao1") %>% vis(.by = "my_var", .meta = my_data$meta) one can see:

Warning message:
In geom_signif(data = p_df, aes(xmin = group1, xmax = group2, annotations = p.adj,  :
  Ignoring unknown aesthetics: xmin, xmax, annotations, and y_position

I guess it is from immunarch's dependencies.