change the position of pvalue in the figure?

[marwa38]

hello .. I am running wilcox_test() on my data but I don't know what is the option that I can use for grouping as in the case of group.by in compare_means()

my codes

my_comparisons <- list(c("marine", "vegetable"))

stat.test <- ps.prev0.gen1.rel.melt %>%
  wilcox_test(Abundance ~ treatment, comparisons = my_comparisons) %>%
  add_significance("p")

# .y.       group1 group2       n1    n2 statistic     p p.signif
# * <chr>     <chr>  <chr>     <int> <int>     <dbl> <dbl> <chr>   
#   1 Abundance marine vegetable   180   170     15397 0.919 ns 

while I want to the results output to be like the following
where I used the grouping (group.by) in compare_means()

compare_means(Abundance ~ treatment,
              group.by = "Genus",
              ps.prev0.gen1.rel.melt,
              p.adjust.method = "BH") 

# # A tibble: 10 × 9
# Genus           .y.       group1 group2         p p.adj p.format p.signif method  
# <fct>           <chr>     <chr>  <chr>      <dbl> <dbl> <chr>    <chr>    <chr>   
#   1 Pseudomonas     Abundance marine vegetable 0.351   0.81 0.351    ns       Wilcoxon
# 2 Lactobacillus   Abundance marine vegetable 0.568   0.81 0.568    ns       Wilcoxon
# 3 Sphingopyxis    Abundance marine vegetable 0.176   0.81 0.176    ns       Wilcoxon
# 4 Photobacterium  Abundance marine vegetable 0.703   0.81 0.703    ns       Wilcoxon
# 5 Yersinia        Abundance marine vegetable 0.680   0.81 0.680    ns       Wilcoxon
# 6 Pediococcus     Abundance marine vegetable 0.438   0.81 0.438    ns       Wilcoxon
# 7 Leuconostoc     Abundance marine vegetable 0.400   0.81 0.400    ns       Wilcoxon
# 8 Bifidobacterium Abundance marine vegetable 0.729   0.81 0.729    ns       Wilcoxon
# 9 Lactococcus     Abundance marine vegetable 0.908   0.91 0.908    ns       Wilcoxon
# 10 Staphylococcus  Abundance marine vegetable 0.0532  0.53 0.053    ns       Wilcoxon

many thanks

[marwa38]

I found the way to do it
but I couldn't change the position of the pvalue on the figure (as I can't see it well in Pseudomonas for example)
your advice please? is very much appreciated

my_comparisons <- list(c("marine", "vegetable"))

stat.test <- ps.prev0.gen1.rel.melt %>%
  group_by(Genus) %>%
  wilcox_test(data =., Abundance ~ treatment) %>%
  adjust_pvalue(method = "BH") %>%
  add_significance("p.adj")

# Add p-values to a boxplot
stat.test <- stat.test %>% add_xy_position(x = "treatment")
ggboxplot(ps.prev0.gen1.rel.melt, x = "treatment", y = "Abundance", color = "Phylum", facet.by = "Genus") +
  stat_pvalue_manual(stat.test, label = "p = {p}{p.adj.signif}")

thanks in advance for your help