为每个箱线图添加中间值

Question

这是文件new.txt

Chr Start   End Name    18NGS31 18MPD168    18NGS21 18NGS29 18NGS33 18NGS38
chr9    1234    1234    ABL1    1431    1   1112    1082    1809    1647
chr9    2345    2345    ASXL1   3885    37  3578    1974    2921    3559
chr9    3456    3456    ETV6    3235    188 2911    1578    2344    2673
chr9    4567    4567    MYD88   3198    187 2860    1547    2289    2621

我正在使用R脚本从第5列起获取箱形图

library(tidyverse)
file <- "new.txt"
df <- read.table(file, header = T, check.names=F)
a <-  df %>%
  gather(key, value, -Chr, -Start, -End, -Name) %>%
  ggplot(aes(x = key, y = value )) +
  geom_boxplot(fill = "orange", colour = "firebrick2") + scale_y_continuous(name="Coverage", limits=c(0, 5000), breaks = seq(0,5000,by = 500)) + scale_x_discrete(name='Samle ID')
a + theme(axis.text.x = element_text(angle = 90, hjust = 1))

我想添加每个箱形图的中位数。

我使用了How to display the median value in a boxplot in ggplot?

的ggplot的geom_text

但是我做不到。

这是我使用的命令

file <- "new.txt"
df <- read.table(file, header = T, check.names=F)
a <-  df %>%
  gather(key, value, -Chr, -Start, -End, -Name)
b <- ggplot(a,aes(x = key, y = value )) +
        geom_boxplot(fill = "orange", colour = "firebrick2") + scale_y_continuous(name="Coverage", limits=c(0, 5000), breaks = seq(0,5000,by = 500)) + scale_x_discrete(name='Samle ID')+
        geom_text(data=a,aes(x= key, y = median(value) , label =median(value)), position=position_dodge(width = 0.8),size = 3, vjust = -0.5,colour="blue")
b + theme(axis.text.x = element_text(angle = 90, hjust = 1))

这是输出

中值计算错误。

Answer 1

问题是您为所有median计算了key（使用2131时得到median(value)的数字）。您可以使用group_by将记录按key分组，然后才可以计算中值（来自summarise包的dplyr函数）：

library(tidyverse)
dataInput  <- gather(df, key, value, -Chr, -Start, -End, -Name)
dataMedian <- summarise(group_by(dataInput, key), MD = median(value))
ggplot(dataInput, aes(key, value)) +
    geom_boxplot() + 
    geom_text(data = dataMedian, aes(key, MD, label = MD), 
              position = position_dodge(width = 0.8), size = 3, vjust = -0.5)