原文链接：使用ggplot绘制柱状图，在柱子中显示数值和显著性

本期教程

获得本期教程示例数据，后台回复关键词：20240628。（PS：在社群中，可获得往期和未来教程所有数据和代码）

往期教程部分内容

写在前面

基于ggplot绘制柱状图，小技巧，很基础的图形。但是，越到后面，会发现，越是基础的图形，我们使用的频率越高。今天的教程是基于发芽指数来绘制，我们模拟一个发芽数和天数，计算出发芽指数。

代码

##'@在柱状图中显示数字
##'@2024.06.28
##'@
##'@小杜的生信笔记

library(ggplot2)
library(dplyr)
library(tidyr)
library(ggplot2)
library(agricolae)

setwd("D:\\BioinfoFile\\小杜的生信笔记\\2024\\20240628_柱状图中显示数据")
##'@此次数据基于种子发芽指数计算公式进行，数据具有随机性，不具有任何意义。
##'@加载数据
data <- read.csv("20240628_inputdata.csv",header = T)

data

相关计算代码

## 转换数据
long_data <- data %>%
  pivot_longer(cols = starts_with("germinated"), names_to = "replicate", values_to = "germinated")
long_data
##计算活力指数
germination_index <- long_data %>%
  group_by(treatment, day) %>%
  summarise(GI = sum(germinated / day)) %>%
  ungroup()

#'@计算各个处理的平均数和标准差
summary_gi <- germination_index %>%
  group_by(treatment) %>%
  summarise(mean_GI = mean(GI), sd_GI = sd(GI))

#'@单因素方差分析
anova_result <- aov(GI ~ treatment + day, data = germination_index)
summary(anova_result)

#'@进行Tukey HSD检验
tukey_result <- HSD.test(anova_result, "treatment", group = TRUE)
print(tukey_result)


# 提取 Tukey HSD 结果中的字母标记
groups <- tukey_result$groups
df_letters <- data.frame(sample = rownames(groups), letters = groups$groups)
##'@修改名称
colnames(df_letters) <- c("treatment","letters")

# 合并均值和字母标记
df_data <- merge(summary_gi, df_letters, by = "treatment")

绘图

ggplot(df_data, aes(x = treatment, y = mean_GI, fill = treatment)) +
  geom_bar(stat = "identity", position = "dodge", color = "black", size = 0.5) +
  ##'@误差线
  geom_errorbar(aes(ymin = mean_GI - sd_GI, ymax = mean_GI + sd_GI), width = 0.15, ## 宽度
                size = 1  ##字体大小
                ) +
  ##'@显示数字
  geom_text(aes(x = treatment, y = mean_GI + sd_GI + 0.5,  ## “+0.5”显示的高度
                label = round(mean_GI, 2)),   ### "round(mean_GI, 2))",其中2，表示数字显示的小数点位数
            size = 5,
            color = 'black') +
  ##'@显示显著性
  geom_text(aes(x = treatment, y = mean_GI + sd_GI + 1.3, label = letters), size = 6, color = "red") +
  theme_bw()+
  scale_fill_manual(values = c("#1f78b4", "#ff7f00", "#4daf4a")) +
  labs(x = NULL, y = "Germination Index")+
  theme(#axis.line = element_line(size = 1),  ## 粗细
    text=element_text(#family = "sans",
      colour ="black",size = 10),
    axis.text.x = element_text(color = "black", size = 12),
    axis.text.y = element_text(color = "black",size = 11),
    axis.ticks = element_line(colour = "black"),
    strip.text = element_text(color = "black",size = 10),
    axis.title = element_text(color = "black",size = 12), ##坐标轴字体大小
    legend.position = "none",
    strip.background = element_blank()
  )

ggsave("20240608_柱状图-显示数字.pdf",width = 6, height = 4)