stat_compare_means 条件 p 值标签导致 ggplot 填充失败

Question

按照this post 的示例，我的目标是仅在 p 值低于某个阈值时标记比较。在终于让它工作之后，我看到它正在抵消之前设置的 ggplot 参数并且不再能够找到填充变量。

我已经包含了一个可重现的示例和我想要的输出。

set.seed(20)
col1<-c(rep('E', each = 8))
col2<-c(rep('R', each = 8))
col3<-c(rep('S', each = 8))
behaviour<-c(col1,col2,col3)
value <- runif(length(behaviour), min=2, max=8)
shannon <- c(rep('Shannon', each = length(behaviour)))
test.data <- data.frame(behaviour, value, shannon)

d <- compare_means(value~behaviour, data = test.data,method = 't.test')
d %<>% mutate(y_pos = c(5,5.5,6),labels = ifelse(p<0.17,p.format,p.signif))

d
.y. group1  group2  p   p.adj   p.format    p.signif    method  y_pos   labels
value   E   R   0.4678791   0.76    0.47    ns          T-test  5.0     ns
value   E   S   0.1559682   0.47    0.16    ns          T-test  5.5     0.16
value   R   S   0.3794209   0.76    0.38    ns          T-test  6.0     ns


shannonviolin<-ggplot(test.data, aes(x = behaviour, y = value)) +
  labs(y= "Shannon",color = " ",size=8)+
  geom_violin(position=position_dodge(width=1.2),alpha = 0.7,scale="width",adjust=0.9,trim=FALSE)+ 
  geom_boxplot(width=0.4,outlier.colour = "transparent")+
  geom_point(aes(fill = behaviour), size = 5, shape = 21, position = position_jitterdodge()) +
  theme_classic()+
  scale_fill_manual(values = c("E" = '#3797a4', "R"= '#96bb7c',"S"= '#944e6c'))+
  theme(text = element_text(size = 18),
        axis.title.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        panel.grid.major.x = element_blank(),
        legend.position = "right",
        axis.text.x=element_blank(),
        axis.ticks.x=element_blank(),
        legend.title = element_blank()
        )+
ylim(0, 14)

shannonviolin+geom_signif(data = as.data.frame(d), tip_length = 0.01, aes(xmin=group1, xmax=group2, annotations=labels,y_position=c(12.4,13,13.6)),manual=TRUE)

这让它开始工作：

但是没有填充颜色。如果我在 ggplot 中指定填充参数：

shannonviolinfill<-ggplot(test.data, aes(x = behaviour, y = value,fill=behaviour)) +
  labs(y= "Shannon",color = " ",size=8)+
  geom_violin(position=position_dodge(width=1.2),alpha = 0.7,scale="width",adjust=0.9,trim=FALSE)+ 
  geom_boxplot(width=0.4,outlier.colour = "transparent")+
  geom_point(aes(fill = behaviour), size = 5, shape = 21, position = position_jitterdodge()) +
  theme_classic()+
  scale_fill_manual(values = c("E" = '#3797a4', "R"= '#96bb7c',"S"= '#944e6c'))+
  theme(text = element_text(size = 18),
        axis.title.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        panel.grid.major.x = element_blank(),
        legend.position = "right",
        axis.text.x=element_blank(),
        axis.ticks.x=element_blank(),
        legend.title = element_blank()
        )+
ylim(0, 14)
shannonviolinfill+geom_signif(data = as.data.frame(d), tip_length = 0.01, aes(xmin=group1, xmax=group2, annotations=labels,y_position=c(12.4,13,13.6)),manual=TRUE)

我得到的错误是

ERROR while rich displaying an object: Error: Aesthetics must be either length 1 or the same as the data (3): fill

理想情况下应该是这样的：

如果有人知道黑客或解决方法，我将不胜感激，因为我整天都在绕着下水道转！

Answer 1

问题是您将fill = behaviour 设为全局aes。但是，您的数据集 d 中没有名为 behaviour 的列。作为一种解决方法，通过将其从 ggplot() 中删除来使其成为本地，而不是在 geom_violin 和 geom_boxcplot 中使用 aes(fill = behaviour)：

set.seed(20)
col1<-c(rep('E', each = 8))
col2<-c(rep('R', each = 8))
col3<-c(rep('S', each = 8))
behaviour<-c(col1,col2,col3)
value <- runif(length(behaviour), min=2, max=8)
shannon <- c(rep('Shannon', each = length(behaviour)))
test.data <- data.frame(behaviour, value, shannon)


library(ggpubr)
#> Loading required package: ggplot2
library(magrittr)
library(ggplot2)

d <- compare_means(value~behaviour, data = test.data,method = 't.test')
d %<>% mutate(y_pos = c(5,5.5,6),labels = ifelse(p<0.17,p.format,p.signif))


shannonviolin<-ggplot(test.data, aes(x = behaviour, y = value)) +
  labs(y= "Shannon",color = " ",size=8)+
  geom_violin(aes(fill = behaviour), position=position_dodge(width=1.2),alpha = 0.7,scale="width",adjust=0.9,trim=FALSE)+ 
  geom_boxplot(aes(fill = behaviour), width=0.4,outlier.colour = "transparent")+
  geom_point(aes(fill = behaviour), size = 5, shape = 21, position = position_jitterdodge()) +
  theme_classic()+
  scale_fill_manual(values = c("E" = '#3797a4', "R"= '#96bb7c',"S"= '#944e6c'))+
  theme(text = element_text(size = 18),
        axis.title.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        panel.grid.major.x = element_blank(),
        legend.position = "right",
        axis.text.x=element_blank(),
        axis.ticks.x=element_blank(),
        legend.title = element_blank()
  )+
  ylim(0, 14)

shannonviolin+geom_signif(data = as.data.frame(d), tip_length = 0.01, aes(xmin=group1, xmax=group2, annotations=labels,y_position=c(12.4,13,13.6)),manual=TRUE)
#> Warning: Ignoring unknown aesthetics: xmin, xmax, annotations, y_position
#> Warning: Removed 141 rows containing missing values (geom_violin).

^{由reprex package (v1.0.0) 于 2021-02-04 创建}