加載R包

1）設(shè)置工作目錄

rm(list=ls())#clear Global Environment
setwd('D:\\桌面\\小提琴圖')

2）安裝、加載R包

#安裝包
# install.packages("ggplot2")
# install.packages("ggpubr")
# install.packages("ggsignif")
# install.packages("tidyverse")
# install.packages("ggprism")
# install.packages("vioplot")
#加載包
library(ggplot2)#繪圖包
library(ggpubr)#基于ggplot2的可視化包，主要用于繪制符合出版要求的圖形
library(ggsignif)#用于P值計(jì)算和顯著性標(biāo)記
library(tidyverse)#數(shù)據(jù)預(yù)處理
library(ggprism)#提供了GraphPad prism風(fēng)格的主題和顏色，主要用于美化我們的圖形
library(vioplot)#小提琴圖繪制包

準(zhǔn)備數(shù)據(jù)

#可加載自己的數(shù)據(jù)，這里我們使用隨機(jī)編寫的數(shù)據(jù)
# df <- read.table("data.txt",header = T,  check.names = F)
#自己隨機(jī)編寫的數(shù)據(jù)
df <- data.frame(
  A_1 = c(2,5,6,5,4,8,6,3,8,9),
  A_2 = c(5,8,6,3,4,7,9,3,6,4),
  B_1 = c(15,10,5,18,12,13,16,14,10,9),
  B_2 = c(25,20,23,15,14,24,20,22,25,26),
  C_1 = c(1,3,6,5,2,3,6,2,4,1),
  C_2 = c(7,8,9,6,7,8,9,6,7,10))
#預(yù)覽數(shù)據(jù)
head(df)

image.png

2）處理數(shù)據(jù)、添加分組信息

#使用tidyverse包對(duì)數(shù)據(jù)進(jìn)行處理
df <- df %>% 
  gather(key = 'samples',value = 'values') #gather()函數(shù)可以把多列數(shù)據(jù)合并成一列數(shù)據(jù)
#添加分組信息
df$group = rep(c("A","B","C"), each = 20)
head(df)#預(yù)覽數(shù)據(jù)

image.png

使用vioplot包進(jìn)行繪圖

??vioplot#查看具體參數(shù)
vioplot(values~samples, data = df, 
        main = "vioplot", # 設(shè)置標(biāo)題
        col=c("#000000", "#be0027", "#cf8d2e","#e4e932","#2c9f45","#371777"),#設(shè)置小提琴顏色
        xlab="Samples", ylab="values") # 軸標(biāo)題

image.png

使用ggplot2包進(jìn)行繪制

1）基本繪圖

p1 <- ggplot(df, aes(x=samples, y=values, fill=samples)) + 
  geom_violin()
p1

image.png

2）添加箱線圖及均值點(diǎn)

p2<-p1+geom_boxplot(alpha=1,outlier.size=0, size=0.3, width=0.2,fill="white")+
  stat_summary(fun="mean",geom="point",shape=21, size=2,fill="blue")
p2

image.png

3）自定義顏色

col=c("#000000", "#be0027", "#cf8d2e","#e4e932","#2c9f45","#371777")
p3<-p2+scale_fill_manual(values = col)
p3

image.png

4）按照分組進(jìn)行分面

p4<-p3+facet_grid(~group,scales = 'free')
p4

image.png

5）顯著性標(biāo)記

p5<-p1+geom_signif(comparisons = list(c("A_1","A_2"),
                                      c("B_1","B_2"),
                                      c("C_1","C_2")),# 設(shè)置需要比較的組
                   map_signif_level = T, #是否使用星號(hào)顯示
                   test = t.test, ##計(jì)算方法
                   size=0.8,color="black")
p5

image.png

結(jié)合ggprism包進(jìn)行個(gè)性化繪圖

p <- ggplot(df, aes(x=samples, y=values, fill=group))+#指定數(shù)據(jù)
  geom_violin(trim = T,position = position_dodge(width = 0.1), scale = 'width')+#繪制小提琴圖函數(shù)
  geom_boxplot(alpha=1,outlier.size=0, size=0.3, width=0.2,fill="white")+#添加箱線圖
  stat_summary(fun="mean",geom="point",shape=21, size=2,fill="blue")+#均值點(diǎn)
  labs(x="Samples",y=NULL)+#標(biāo)題
  # geom_jitter(width = 0.2,size=2,pch=20,color="black")+#添加抖動(dòng)點(diǎn)
  theme_prism(palette = "flames",
              base_fontface = "plain", # 字體樣式，可選 bold, plain, italic
              base_family = "serif", # 字體格式，可選 serif, sans, mono, Arial等
              base_size = 16,  # 圖形的字體大小
              base_line_size = 0.8, # 坐標(biāo)軸的粗細(xì)
              axis_text_angle = 45)+ # 可選值有 0，45，90，270
  scale_fill_prism(palette = "flames")+
  geom_signif(comparisons = list(c("A_1","A_2"),#顯著性
                                 c("B_1","B_2"),
                                 c("C_1","C_2")),# 設(shè)置需要比較的組
              map_signif_level = T, #是否使用星號(hào)顯示
              test = "t.test", ##計(jì)算方法
              tip_length = c(c(0.01,0.01),
                             c(0.01,0.01),
                             c(0.01,0.01)),#橫線下方的豎線設(shè)置
              size=0.8,color="black")
p

image.png