跟着PC学作图 | 小提琴图+Tufte箱形图+折线图的绘制教程

一、数据

本期教程是基于ggplot()绘制，数据类型也符合ggplot（）函数类型即可。

本期，直接使用的文章中的数据。

二、绘图

导入相关包

library(ggplot2)
library(tidyverse)
library(reshape)
library(agricolae)

library(ggthemes)

导入数据

diam <- read.csv("inputdata.csv", header = TRUE, sep = ',', stringsAsFactors=FALSE)
head(diam)

数据整理

此步更具自己数据需求操作

### Add groups to the data
diam$Groups <- paste(diam$Species,diam$CO2,diam$Day,sep="_")
diam$Groups <- factor(diam$Groups,levels = unique(gtools::mixedsort(diam$Groups)))

差异比较

maxDiam = diam %>% group_by(Groups) %>% summarize(MaxDiameter=max(diameter))

### Do tukey tests
hsd_diameter=HSD.test(aov(diameter~Groups,data=diam), "Groups", group=T)
hsd_diameter$groups <- hsd_diameter$groups[levels(diam$Groups),]
tukeyDiameter <- data.frame(rownames(hsd_diameter$groups),
                            do.call("rbind",strsplit(rownames(hsd_diameter$groups),"_")),
                            hsd_diameter$groups,stringsAsFactors = T)
colnames(tukeyDiameter) <- c("Groups","Species","CO2","Day","median_diameter","groups")

tukeyDiameter <- left_join(tukeyDiameter,meanDiam,by="Groups")
head(tukeyDiameter)

> head(tukeyDiameter)
                         Groups Species      CO2 Day median_diameter groups
M82_ambient_7     M82_ambient_7     M82  ambient   7        321.9840     bc
M82_ambient_10   M82_ambient_10     M82  ambient  10        390.9108     ab
M82_ambient_13   M82_ambient_13     M82  ambient  13        430.4615      a
M82_elevated_7   M82_elevated_7     M82 elevated   7        316.3562     bc
M82_elevated_10 M82_elevated_10     M82 elevated  10        448.0713      a
M82_elevated_13 M82_elevated_13     M82 elevated  13        443.9278      a

ggplot绘图

箱线图

plotGG <- ggplot(diam,aes(x=Groups,y=diameter)) +
  scale_fill_manual(values=c("skyblue1", "black")) + scale_color_manual(values=c("skyblue1", "black")) +
  geom_violin(aes(color=paste(CO2)),position=position_dodge(1),trim = F,width=1)

Tufte箱形图

plotGG + geom_tufteboxplot(position=position_dodge(1),outlier.colour="transparent", width = 1,color="black")

line图

plotGG02 + geom_line(data=tukeyDiameter, aes(x=Groups, y=median_diameter,group = paste(CO2,Species)),alpha=0.5)

添加显著性差异

plotGG03 <- plotGG02 + geom_text(data=tukeyDiameter, aes(x=Groups, y=(maxDiam$MaxDiameter)*1.25,label=groups,group=NULL),vjust=0,color="black")

进行美化

plotGG03 +theme_bw()+
  ggtitle("Root diameter change by species in response to eCO2 over time") + 
  xlab('')+
  ylab(expression(paste("Root diameter (",mu,"m)"))+
  theme(#legend.position="bottom",
    legend.text = element_text(size=12),
    axis.text.y = element_text(size=12, colour="black", family = "sans", angle = 0), 
    axis.text.x = element_text(size=12, colour="black", family = "sans", angle = 45, hjust = 1),
    axis.title= element_text(size=12),
    strip.text.x = element_text(size=12, angle = 0),
    strip.text.y = element_text(size=12, angle = 0),
    plot.title = element_text(size=12, angle = 0))

绘图全部代码

ggplot(diam,aes(x=Groups,y=diameter)) +
  scale_fill_manual(values=c("skyblue1", "black")) + scale_color_manual(values=c("skyblue1", "black")) +
  geom_violin(aes(color=paste(CO2) ),position=position_dodge(1),trim = F,width=1) + 
  #geom_boxplot(aes(color=paste(CO2)),position=position_dodge(1),width=0.09,outlier.shape = NA) + 
  geom_tufteboxplot(position=position_dodge(1),outlier.colour="transparent", width = 1,color="black") + 
  #geom_dotplot(aes(fill=CO2),binaxis='y', stackdir='center',position=position_dodge(1),dotsize = 0.5)  + #Looks cleaner than with
  #geom_jitter(aes(color=paste(CO2)),width = 0.05,size=0.75) + 
  geom_line(data=tukeyDiameter, aes(x=Groups, y=median_diameter,group = paste(CO2,Species)),alpha=0.5) +
  facet_grid(.~Species,scales = "free_x",as.table = T) +
  coord_cartesian(ylim = c(min(diam$diameter)*.6, max(diam$diameter)*1.5)) +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ## 添加显著性差异
  geom_text(data=tukeyDiameter, aes(x=Groups, y=(maxDiam$MaxDiameter)*1.25,label=groups,group=NULL),vjust=0,color="black")+
  theme_bw()+
  ggtitle("Root diameter change by species in response to eCO2 over time") + 
  xlab('')+
  ylab(expression(paste("Root diameter (",mu,"m)")))+
  theme(#legend.position="bottom",
    legend.text = element_text(size=12),
    axis.text.y = element_text(size=12, colour="black", family = "sans", angle = 0), 
    axis.text.x = element_text(size=12, colour="black", family = "sans", angle = 45, hjust = 1),
    axis.title= element_text(size=12),
    strip.text.x = element_text(size=12, angle = 0),
    strip.text.y = element_text(size=12, angle = 0),
    plot.title = element_text(size=12, angle = 0))

往期文章：

1. 最全WGCNA教程（替换数据即可出全部结果与图形）

WGCNA分析 | 全流程分析代码 | 代码一

WGCNA分析 | 全流程分析代码 | 代码二

WGCNA分析 | 全流程代码分享 | 代码三

2. 精美图形绘制教程

精美图形绘制教程