How to add p values into grouped charts in ggplot? - r

Question

When I want to add p values into my plots:
library(tidyverse)
library(ggpubr)
library(rstatix)
stat.test3 <- MP %>%
group_by(TBI) %>%
wilcox_test(age ~ mp_1) %>%
adjust_pvalue(method = "bonferroni") %>%
add_significance("p.adj")%>%
mutate(y.position = 35)
C2<- ggplot(data=MP, aes(x=TBI, y=age, fill=mp_1))+
geom_violin()+
geom_boxplot(width=.2, fatten=NULL, position = position_dodge(0.9))+
stat_summary(fun="median", geom="point", position = position_dodge(0.9))+
stat_summary(fun.data = "mean_se", geom = "errorbar", width=.1, position = position_dodge(0.9))+
scale_fill_brewer(name="Mind-pop", palette = "Accent")
C2+ stat_pvalue_manual(stat.test3, xmin = "TBI",xmax = NULL)
it gives me this error:
Error in FUN(X[[i]], ...) : object 'mp_1' not found
This error is shown after adding stat_pvalue to the object.
How should I fix it?

Answer 1

I'm not familiar with ggpubr so can't say I understand the underlying issue but it seems like color=mp_1 instead of fill=mp_1 might fix your issue. This is in the following line:
C2 <- ggplot(data=MP, aes(x=TBI, y=age, color=mp_1)).
The full code is below. I've also changed y.position so that the significance is at the top of the plot.
MP <- structure(list(age = c(55L, 54L, 56L, 60L, 55L, 53L, 61L, 56L,
58L, 58L, 56L, 58L, 58L, 58L, 59L, 57L, 56L, 60L, 57L, 58L, 61L,
60L),
mp_1 = structure(c(2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("No", "Yes"), class = "factor"),
TBI = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("HC",
"TBI"), class = "factor")), class = "data.frame", row.names = c(NA, -22L))
library(tidyverse)
library(ggpubr)
library(rstatix)
stat.test3 <- MP %>%
group_by(TBI) %>%
wilcox_test(age ~ mp_1) %>%
adjust_pvalue(method = "bonferroni") %>%
add_significance("p.adj") %>%
mutate(y.position = 61.5)
C2 <- ggplot(data=MP, aes(x=TBI, y=age, color=mp_1))+
geom_violin() +
geom_boxplot(width=.2, fatten=NULL, position = position_dodge(0.9))+
stat_summary(fun="median", geom="point", position = position_dodge(0.9))+
stat_summary(fun.data = "mean_se", geom = "errorbar", width=.1, position = position_dodge(0.9))+
scale_fill_brewer(name="Mind-pop", palette = "Accent")
C2 + stat_pvalue_manual(stat.test3, xmin = "TBI",xmax = NULL)