跟着Microbiome学绘图(1) 个性化组合进化树与热图

2022-09-21 14:38:20 浏览数 (1)

❝今天来介绍如何对进化树枝进行折叠，将属于同一分支的折叠，从下面的论文中挑出一份数据通过一个小例子来展示 ❞

加载R包

代码语言：javascript复制
library(tidyverse)
library(ggtree)
library(ggdendro)
library(patchwork)

加载数据

代码语言：javascript复制
df <- read_csv("Figure5-metabolicfunctions_logtpm.csv") %>% dplyr::rename(tax=`...1`) %>% 
  column_to_rownames(var="tax")

绘制进化树

  • 此处先选择需要的点，后对其进行折叠，具体参数请参考ggtree官方文档，https://yulab-smu.top/treedata-book/chapter6.html
代码语言：javascript复制
tree <- hclust(dist(df)) %>% ggtree() %>% 
  collapse(174, 'min', fill="#E41A1C")  %>% 
  collapse(173, 'max', fill="#1E90FF") %>% 
  collapse(146, 'mix', fill="#FF8C00") %>% 
  collapse(141, 'mixed', fill="#4C005C") %>% 
  collapse(155, 'min', fill="#003380") %>% 
  collapse(154, 'min', fill="#FF8C00") %>%
  collapse(155, 'min', fill="#FF8C00") %>%
  collapse(152, 'mixed', fill="#740AFF") %>%
  collapse(151, 'min', fill="#FF8C00") %>% 
  collapse(150, 'min', fill="#8F7C00") %>% 
  collapse(143, 'min', fill="#E41A1C") %>% 
  collapse(144, 'min', fill="#94FFB5") %>% 
  collapse(159, 'min', fill="#0075DC") %>% 
  collapse(158, 'min', fill="#00FFFF") %>% 
  collapse(156, 'min', fill="#E41A1C") %>% 
  collapse(148, 'min', fill="#8F7C00") %>% 
  collapse(140, 'min', fill="#E41A1C")

提取聚类标签

代码语言：javascript复制
hrdata <- hclust(dist(df)) %>% dendro_data(.,type="rectangle")
hcdata <- hclust(dist(t(df))) %>% dendro_data(.,type="rectangle")

定义热图数据

代码语言：javascript复制
df2 <- read_csv("Figure5-metabolicfunctions_logtpm.csv") %>% dplyr::rename(tax=`...1`) %>% 
  pivot_longer(-tax)

自定义因子

代码语言：javascript复制
df2$tax <- factor(df2$tax,levels = hrdata$labels %>% select(label) %>% pull())
df2$name <- factor(df2$name,levels = hcdata$labels %>% select(label) %>% pull())

绘制热图

代码语言：javascript复制
heatmap <- df2 %>% ggplot(aes(name,tax,fill=value)) 
  geom_tile() 
  labs(x=NULL,y=NULL) 
  scale_y_discrete(expand=c(0,0),position="left") 
  scale_x_discrete(expand=c(0,0)) 
  scale_fill_gradientn(colours = rev(RColorBrewer::brewer.pal(11,"RdBu"))) 
  theme(axis.text.x=element_text(color="black",angle=90,vjust=0.5,size=8,hjust=1),
        axis.text.y=element_blank(),
        axis.ticks = element_blank(),
        legend.title = element_blank(),
        legend.text = element_text(size=8,color="black")) 
  guides(fill=guide_colorbar(direction = "vertical",reverse = F,barwidth = unit(.6, "cm"),
                             barheight = unit(18.5,"cm")))

拼图

代码语言：javascript复制
tree   heatmap  plot_layout(widths = c(.3,1))、
官方文档

0 人点赞