前两天在公众号植物与根际微生物生态看到一篇转载的文章，关于聚类与物种组成柱状图的：

0.png

翻看了作者的代码，基本是用R base写的，我想着能不能用Y数的ggtree​结合ggplot2来完成。数据使用的是这个公众号提供的数据（表示感谢）。

绘制聚类数

 library(tidyverse)
 library(ggplot2)
 library(ggtree)
 library(treeio)
 library(ggsci)
 library(cowplot)
 ​
 # 导入OTU文件
 otu = read.table('phylum_top10.txt', header =  T)
 ​
 # 计算距离后均值聚类并建树及可视化
 tree = hclust(vegan::vegdist(t(otu), method = 'bray'), 
  method = 'average') %>%
  as.phylo()
 # 选择节点，方便后续分开上色
 tree = groupClade(tree, .node=c(16))
 ​
 # 绘制聚类图
 p1 = ggtree(tree, aes(color=group, linetype=group)) + 
  geom_tiplab(aes(color=group))
  # +geom_text2(aes(subset=!isTip, label=node), hjust=-.3)</pre>

2.png

绘制物种组成柱状图

 p2 = otu %>%
  mutate(phylum = rownames(otu)) %>%
  reshape2::melt(id.vars = 'phylum') %>%
  ggplot(aes(variable, value, fill = phylum))+
  geom_bar(stat = 'identity', position = 'fill')+
  scale_x_discrete(limits = c('t1','t2','t5','t4','t3','t6',
  'c1','c2','c6','c4','c3','c5'))+
  scale_fill_igv()+
  scale_y_continuous(expand = c(0,0))+
  scale_y_continuous(labels = scales::percent)+
  coord_flip()+
  theme_classic()+
  theme(axis.ticks.y = element_blank(),
  axis.title.y = element_blank(), 
  axis.text.y = element_blank(), 
  axis.line = element_blank())+
  labs(y = 'Percentage')

3.png

拼图

 ggdraw()+
  draw_plot(p1, 0, 0.06, 0.5, 0.95)+
  draw_plot(p2, 0.49, 0, 0.5, 1)</pre>

1.png

参考文献

[1] Yu, Guangchuang, et al. "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data." Methods in Ecology and Evolution 8.1 (2017): 28-36.

点击下载示例数据与完整代码

https://www.jianguoyun.com/p/DcRYfHoQsq2iCBiP8ZYD