复现NC图表：ggplot做配对连线云雨

在一篇《nature communication》文章上看到这个图表，乍一看，这不就是云雨图嘛，所以准备复现一下。这个图的特点是：1、云雨图但是连中间的箱线图都是一半（这个一般云雨图包办不到）。2、配对连线。

（reference：Multi-omics identify falling LRRC15 as a COVID-19 severity marker and persistent pro-thrombotic signals in convalescence）

本着我看图是拿显微镜的优秀品质，我找到了这篇文章当初上传在预印本上的版本，发现这个图其实很拙劣，之所以小提琴图和箱线图都是一半，是因为作者在中间加入了一个很明显没有p掉的矩阵。这瞬间让我有了思路。我们常规作图，只需要在适当位置加入分面即可。示例数据及代码已上传群文件！

说干就干，上图：效果杠杠的

setwd('D:/KS项目/公众号文章/配对云雨图')
df <- read.csv('df.csv', header = T)
library(ggplot2)

df$Family.ID <- as.factor(df$Family.ID)
ggplot(df,aes(x=Disease.state,y=Richness,fill=Disease.state))+
  geom_violin(width =0.8, color=NA)+
  geom_boxplot(alpha =0.5,size=1,outlier.shape = NA,width=0.2)+
  geom_rect(aes(xmin = 0.98, 
                ymin = -Inf,
                xmax = 2.02, 
                ymax = Inf),
            fill = "white", 
            size =1.5)+
  geom_jitter(aes(group=Family.ID,color=Disease.state),
              size = 2,
              shape=16,
              stroke = 0.15, 
              show.legend = FALSE, 
              position = position_dodge(0.05))+
  geom_line(aes(group = Family.ID), 
            color = 'grey40', 
            lwd = 0.5,
            position = position_dodge(0.05))+
  theme_bw() + 
  theme(text = element_text(size=10, colour = "black")) + 
  theme(panel.grid =element_blank(),
        axis.text.x = element_text(colour = "black", size = 14),
        axis.text.y = element_text(colour = "black", size = 14),
        axis.title.y = element_text(color = 'black', size = 14),
        axis.title.x = element_blank(),
        legend.position = 'none')+
  labs(title = "", y = "Expression", x=" ")+
  scale_fill_manual(values = c('#E69F00', "#009E73"))

后来发现有个R包，可以将很多ggplot图做成半个，一样的效果：

library(gghalves)
ggplot(df,aes(x=Disease.state,y=Richness,fill=Disease.state))+
  geom_half_violin(data=subset(df, Disease.state=='Patient'),
                   position = position_nudge(x = 0),side="l",color=NA)+
  geom_half_boxplot(data=subset(df, Disease.state=='Patient'),
                    position = position_nudge(x = 0),side='l', width=0.2)+
  geom_half_violin(data=subset(df, Disease.state=='Relative'),
                   position = position_nudge(x = 0),side="r",color=NA)+
  geom_half_boxplot(data=subset(df, Disease.state=='Relative'),
                    position = position_nudge(x = 0),side='r', width=0.2)+
  geom_jitter(aes(group=Family.ID,color=Disease.state),
              size = 2,
              shape=16,
              stroke = 0.15, 
              show.legend = FALSE, 
              position = position_dodge(0.05))+
  geom_line(aes(group = Family.ID), 
            color = 'grey40', 
            lwd = 0.5,
            position = position_dodge(0.05))+
  theme_bw() + 
  theme(text = element_text(size=10, colour = "black")) + 
  theme(panel.grid =element_blank(),
        axis.text.x = element_text(colour = "black", size = 14),
        axis.text.y = element_text(colour = "black", size = 14),
        axis.title.y = element_text(color = 'black', size = 14),
        axis.title.x = element_blank(),
        legend.position = 'none')+
  labs(title = "", y = "Expression", x=" ")+
  scale_fill_manual(values = c('#E69F00', "#009E73"))

至于云雨图啥的，百度一下，有X种做法，感兴趣的可以学习。觉得小编内容有用的、有意思的，点赞、分享、关注一下呗