使用rstatix在ggplots图上的不正确p值位置

Question

我很难使用ggplot将p值放置在rstatix的y轴上的正确位置。我可以让包作者的博客上提供的示例工作得很好，但是当我更改值时，位置是不正确的。以下是工作版本：

library(tidyverse)
library(rstatix)

##Example provided by the package author which works correctly

df <- ToothGrowth%>%
  as_tibble()

#Check df
df

#Stats calculation
stat.test <- df %>%
  group_by(dose) %>%
  t_test(len ~ supp) %>%
  adjust_pvalue(method = "bonferroni") %>%
  add_significance()

# Make facet and add p-values
stat.test <- stat.test %>% add_xy_position(x = "supp", fun = "max")

#Check p value positions - y.position looks good
stat.test

#Plot
ggplot(df, aes(x = supp, y = len)) +
  geom_boxplot() +
  geom_jitter() +
  facet_wrap( ~ dose, scales = "free") +
  stat_pvalue_manual(stat.test, hide.ns = F,
                     label = "{p.adj}")

但是，当我改变值时，p值的位置太高了。

## My example which plots incorrectly

##--- This is a very inelegant way to change the values!!
df <- ToothGrowth %>%
  mutate(helper = paste0(supp, dose))

df$RecordingNo <- ave(seq.int(nrow(df)), df$helper, FUN = seq_along)

df <- df %>%
  select(-helper) %>%
  pivot_wider(names_from = c(dose), values_from = len) %>%
  mutate(`0.5` = `0.5` * 0.1) %>%
  mutate(`2` = `2` * 10) %>%
  select(-RecordingNo) %>%
  pivot_longer(-supp) %>%
  rename(len = value, dose = name) %>%
  mutate(dose = as_factor(dose)) %>%
  as_tibble()

#Check df
df

##------

#This code is exactly the same as the working code above.

#Stats calculation
stat.test <- df %>%
  group_by(dose) %>%
  t_test(len ~ supp) %>%
  adjust_pvalue(method = "bonferroni") %>%
  add_significance()

# Make facet and add p-values
stat.test <- stat.test %>% add_xy_position(x = "supp", fun = "max")

#Check p value positions - y.position looks incorrect
stat.test

ggplot(df, aes(x = supp, y = len)) +
  geom_boxplot() +
  geom_jitter() +
  facet_wrap( ~ dose, scales = "free") +
  stat_pvalue_manual(stat.test, hide.ns = F,
                     label = "{p.adj}")

我想在第二个数据文件中有一个不同之处，它导致了这些问题，但我无法弄清楚。谢谢!

Answer 1

与facet_wrap上的facet_wrap选项一样，在add_xy_position上有一个控制p值位置的scales选项。由于我使用的是"facet_wrap(...,scales = "free")"，所以我应该使用add_xy_position(...,scales = "free")来确保位置匹配。

在我的例子中：

stat.test <- stat.test %>% add_xy_position(x = "supp", fun = "max",scales = "free")

ggplot(df, aes(x = supp, y = len)) +
  geom_boxplot() +
  geom_jitter() +
  facet_wrap( ~ dose, scales = "free") +
  stat_pvalue_manual(stat.test, hide.ns = F,
                     label = "{p.adj}")

作者的吉特布页面的回答。