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

General
1

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: Add P-values and Significance Levels to ggplots - Articles - STHDA but I cont want a wilcoxon or t.test for pairwise comparison...

2

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!

3

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