如何使用stat_pvalue_manual将rstatix的wilcox_test结果添加到ggboxplot()中？
如何使用stat_pvalue_manual将rstatix的wilcox_test结果添加到ggboxplot()中？
提问于 2019-06-27 21:06:39
我正在尝试创建一个箱线图，并手动将p值添加到箱图之间的每次比较中：
#I have the following boxplot
ToothGrowth%>%ggplot(aes(x=dose, y=len, fill=supp))+
geom_boxplot()
#I would like to do a wilcoxon sum rank test on the data and label each comparison between OJ and VC
stat.test <- ToothGrowth%>%group_by(dose)%>%wilcox_test(len~supp, p.adjust.method = 'BH')%>%
mutate(y.position = c(29, 35, 39))
stat.test
#I try to add the p-values to my boxplots
ToothGrowth%>%ggplot(aes(x=dose, y=len, fill=supp))+
geom_boxplot()+
stat_pvalue_manual(stat.test, label = 'p')
#However I get the following error:
# Error in FUN(X[[i]], ...) : object 'supp' not foundStack Overflow用户
回答已采纳
发布于 2019-07-02 04:51:19
您需要在geom_boxplot()中指定fill参数，而不是在ggplot()中。
安装最新开发版本的rstatix和ggpubr，然后尝试以下R代码。
# Required packages
library(ggpubr) # https://github.com/kassambara/ggpubr
library(rstatix) # https://github.com/kassambara/rstatix
# Stat test
ToothGrowth$dose <- as.factor(ToothGrowth$dose)
stat.test <- ToothGrowth %>%
group_by(dose) %>%
wilcox_test(len~supp, p.adjust.method = 'BH') %>%
mutate(y.position = c(29, 35, 39))
stat.test
# Plot + pvalue
bxp <- ggplot(ToothGrowth, aes(x = dose, y = len)) +
geom_boxplot(aes(fill = supp))
bxp + stat_pvalue_manual(stat.test, x = "dose", label = 'p')
# Add automatically x and y positions
stat.test <- ToothGrowth %>%
group_by(dose) %>%
wilcox_test(len~supp, p.adjust.method = 'BH') %>%
add_xy_position(x = "dose")
bxp + stat_pvalue_manual(stat.test, label = 'p', tip.length = 0)
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原文链接：
https://stackoverflow.com/questions/56791735
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