CODEWITHSUNDEEP
rggplot2ggpubr
user2814482
user2814482

Reputation: 651

error with stat_compare_means and multiple groups

I would like to label my boxplots with pvalues.

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")

Upvotes: 0

Views: 7623

Answers (1)

Good Fit
Good Fit

Reputation: 1316

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)

enter image description here 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)`

Upvotes: 3

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