problems plotting p-values from conover test (Dunn's works fine)

Cross-posted at


I am having some trouble with an error message I can't solve.

I use the following code in to run a Kruskal Wallis in R and then do a pairwise comparison using Dunn's:

    res.kruskal <- mydata %>% kruskal_test(values ~ group)
    res.kruskal
    stat.test <- mydata %>% dunn_test(values ~ group, p.adjust.method = "hochberg") 
    stat.test
    stat.test <- stat.test %>% add_xy_position(x = "group")

I then use this result to plot out the significances like so:

    ggboxplot(mydata, x = "group", y = "values, fill = "group") +
      stat_pvalue_manual(stat.test, hide.ns = FALSE)

And get is nice looking plot (hooray!)
https://i.stack.imgur.com/cRAZ9.png

But the Cover Test is apparently more powerful and preferred over Dunn's... (any opinions on this would be welcome too!). Running the following code returns an error:

    res.kruskal <- immdatamed %>% kruskal_test(LplastinTL ~ group)
    res.kruskal
    attach(immdatamed)
    stat.test <- conover.test(LplastinTL, group, method = "hochberg") 
    stat.test
    stat.test <- stat.test %>% add_xy_position(x = "group")
    detach(immdatamed)
stat.test <- stat.test %>% add_xy_position(x = "group")
Error in asserttat_group_columns_exists(test) : 
  data should contain group1 and group2 columns

I can't figure this out... I can run the Conover test fine but can't solve the above error to get it to work with ggboxplot.

I would actually prefer to use the more aesthetically pleasing ggplot & geom_boxplot but can't get that to interface with Dunn_test at all...

Any solutions would be most welcome!

Thank you

P.S. I was using this with ggplot: http://www.sthda.com/english/articles/24-ggpubr-publication-ready-plots/76-add-p-values-and-significance-levels-to-ggplots but I cont want a wilcoxon or t.test for pairwise comparison...

The problem was solved by Chuck P over on the StackExchange site, see cross-post link above.

If anyone has any ideas on how to get Chuck P's solution to work in ggplot that would be most appreciated.

Thanks and happy weekend!

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.