Collectives™ on Stack Overflow

Find centralized, trusted content and collaborate around the technologies you use most.

Teams

Q&A for work

Connect and share knowledge within a single location that is structured and easy to search.

Here is my code:

ggplot(df_annot,aes(x=Insect,y=index,fill=Fungi))+geom_boxplot(alpha=0.8)+
  geom_point(aes(fill=Fungi),size = 3, shape = 21,position = position_jitterdodge(jitter.width = 0.02,jitter.height = 0))+
  facet_wrap(~Location,scales="free" )+
  stat_compare_means(aes(group="Insect"))+
  guides(fill=guide_legend("M. robertii")) +
  scale_x_discrete(labels= c("I+","I-","soil alone"))+
  ylab(index_name)+
  theme(plot.title = element_text(size = 18, face = "bold"))+
  theme(axis.text=element_text(size=14),
        axis.title=element_text(size=14)) + 
  theme(legend.text=element_text(size=14),
        legend.title=element_text(size=14)) +
  theme(strip.text.x = element_text(size = 14))
Here is the error message that I'm getting:
  
Warning messages:

  1: Unknown or uninitialised column: 'p'.

  2: Computation failed in stat_compare_means(): argument "x" is missing, with no default

  3: Unknown or uninitialised column: 'p'.

  4: Computation failed in stat_compare_means(): argument "x" is missing, with no default
I've tried moving around the aes() from the main ggplot call to the boxplot call.  I've tried different inherit.aes in the stat_compare_means().
I've tried first subsetting the root section and making them separately , but the same error.
Any help is appreciated.
thanks
here is my data:
> dput(df_annot)
structure(list(Location = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L), .Label = c("Root", "Rhizospheric Soil"
), class = "factor"), Bean = structure(c(1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("Bean", "No bean"), class = "factor"), 
Fungi = structure(c(2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 
2L, 2L), .Label = c("M+", "M-"), class = "factor"), Insect = structure(c(2L, 
2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("Insect", 
"NI"), class = "factor"), index = c(2.90952191983974, 3.19997588762484, 
2.96753469534499, 2.93030877512644, 2.72220793003196, 3.09008037591454, 
2.63687890737919, 2.73583925812843, 3.06766793411045, 3.26431040286099, 
3.03361194852963, 2.9181623054061)), row.names = c("S-B1", 
"S-B2", "S-B3", "S-BF-1", "S-BF-2", "S-BF-3", "S-BFi-1", "S-BFi-2", 
"S-BFi-3", "S-Bi-1", "S-Bi-2", "S-Bi-3"), class = "data.frame")
A possible and easy fix to your error maybe to use the exact variable name (i.e. remove the double quotes from the variable name) rather that the quoted variable name (i.e. character) in the stat_compare_means (), so the function should look like this:
stat_compare_means(aes(group=Insect))
A working example using ggboxplot() is as follows: 
library(ggpubr)
boxplot <- ggboxplot(ToothGrowth, x = "dose", y = "len", add = "jitter",
                             color = "supp", group="supp", palette = "jco", legend.title="Supplier")
boxplot <- boxplot + stat_compare_means(aes(group=supp), label = "p.signif", method="wilcox.test", hide.ns=T, paired=F)
print(bxp.legend)
There is a warning message for the above example, but I do not know how improve the code to remove the warning message:

`cols` is now required.
Please use `cols = c(p)` 
        
Thanks for contributing an answer to Stack Overflow!
Please be sure to answer the question. Provide details and share your research!
But avoid …
Asking for help, clarification, or responding to other answers.
Making statements based on opinion; back them up with references or personal experience.
To learn more, see our tips on writing great answers.