R语言 | 使用最简单方法添加显著性ggpubr包

news2024/11/28 20:39:59

本期教程原文：使用最简单方法添加显著性ggsignif包

本期教程

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往期教程部分内容

代码

##
library(ggplot2)
library(tidyverse)
library(ggpubr)
library(dplyr)
library(multcompView)
library(ggbreak)
library(data.table)

数据

#'@数据
set.seed(123)  # 设置随机种子以确保结果可重复
samples <- c("CK", "80-1", "4-7", "4-14", "4-60", "20-7", "20-14", "20-60")
mean_values <- c(3, 2.5, 4, 2, 1.5, 4.5, 2.8, 3.5)
data_matrix <- data.frame(
  sample = rep(samples, each = 6),
  value = unlist(lapply(mean_values, function(mu) rnorm(6, mean = mu, sd = 0.3)))
)

若是宽数据，转换长数据即可，可看我们的教程：https://mp.weixin.qq.com/s/i8x0WTcXTrVgD7NGBE3hcA

绘图

##'@固定因子
data_matrix$sample <- factor(data_matrix$sample, levels = c("CK","80-1","4-7","20-7","4-14","20-14","4-60","20-60"))

ggplot(data_matrix, aes(x = sample, y = value, fill = sample)) +
  stat_summary(fun.data = mean_sd, geom = "errorbar", width = 0.15, size = 1) +
  geom_bar(color = "black", stat = "summary", fun = mean, position = "dodge", size = 0.5) +
  ##'@Y轴从0开始
  scale_y_continuous(expand = c(0,0))+
  #theme_classic()+
  #theme_test(base_size = 14)+
  theme_bw(base_size = 14)+
  ## 差异比较组合
  stat_compare_means(comparisons = list(c("CK","80-1"),
                                        c("CK","4-7"),
                                        c("CK","4-14"),
                                        c("CK","4-60"),
                                        c("CK","20-7"),
                                        c("CK","20-14"),
                                        c("CK","20-60")),
                     tip.length = 0.02,
                     method = "wilcox.test", ## t.test， wilcox.test，anova，kruskal.test
                     label = "p.format"   ## p.signif：显示显著性星号,p.format：显示数字
                     )+
  
  scale_fill_manual(values = c("#1f78b4","#ff7f00","#4daf4a",
                               "#fb8072", "#8da0cb",
                               "#bf5b17","#b2df8a","#c8c9c9","#7570b3"))+
  labs(x = NULL,y = "Expression level of genes (FPKM)")+
  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 = 10),
    axis.text.y = element_text(color = "black",size = 10),
    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()
  )