加載R包
1）設置工作目錄
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值計算和顯著性標記
library(tidyverse)#數(shù)據預處理
library(ggprism)#提供了GraphPad prism風格的主題和顏色，主要用于美化我們的圖形
library(vioplot)#小提琴圖繪制包
準備數(shù)據
#可加載自己的數(shù)據填具，這里我們使用隨機編寫的數(shù)據
# df <- read.table("data.txt",header = T, check.names = F)
#自己隨機編寫的數(shù)據
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))
#預覽數(shù)據
head(df)
image.png
2）處理數(shù)據卢未、添加分組信息
#使用tidyverse包對數(shù)據進行處理
df <- df %>%
gather(key = 'samples',value = 'values') #gather()函數(shù)可以把多列數(shù)據合并成一列數(shù)據
#添加分組信息
df$group = rep(c("A","B","C"), each = 20)
head(df)#預覽數(shù)據
image.png
使用vioplot包進行繪圖
??vioplot#查看具體參數(shù)
vioplot(values~samples, data = df,
main = "vioplot", # 設置標題
col=c("#000000", "#be0027", "#cf8d2e","#e4e932","#2c9f45","#371777"),#設置小提琴顏色
xlab="Samples", ylab="values") # 軸標題
image.png
使用ggplot2包進行繪制
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
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）按照分組進行分面
p4<-p3+facet_grid(~group,scales = 'free')
p4
image.png
5）顯著性標記
p5<-p1+geom_signif(comparisons = list(c("A_1","A_2"),
c("B_1","B_2"),
c("C_1","C_2")),# 設置需要比較的組
map_signif_level = T, #是否使用星號顯示
test = t.test, ##計算方法
size=0.8,color="black")
p5
image.png
結合ggprism包進行個性化繪圖
p <- ggplot(df, aes(x=samples, y=values, fill=group))+#指定數(shù)據
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
labs(x="Samples",y=NULL)+#標題
# geom_jitter(width = 0.2,size=2,pch=20,color="black")+#添加抖動點
theme_prism(palette = "flames",
base_fontface = "plain", # 字體樣式陶因，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, # 坐標軸的粗細
axis_text_angle = 45)+ # 可選值有 0巷嚣，45喘先，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")),# 設置需要比較的組
map_signif_level = T, #是否使用星號顯示
test = "t.test", ##計算方法
tip_length = c(c(0.01,0.01),
c(0.01,0.01),
c(0.01,0.01)),#橫線下方的豎線設置
size=0.8,color="black")
p
image.png
