❝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 ❞
library(tidyverse)
library(ggtree)
library(ggdendro)
library(patchwork)
df <- read_csv("Figure5-metabolicfunctions_logtpm.csv") %>% dplyr::rename(tax=`...1`) %>%
column_to_rownames(var="tax")
ggtree
官方文档,https://yulab-smu.top/treedata-book/chapter6.html
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")
hrdata <- hclust(dist(df)) %>% dendro_data(.,type="rectangle")
hcdata <- hclust(dist(t(df))) %>% dendro_data(.,type="rectangle")
df2 <- read_csv("Figure5-metabolicfunctions_logtpm.csv") %>% dplyr::rename(tax=`...1`) %>%
pivot_longer(-tax)
df2$tax <- factor(df2$tax,levels = hrdata$labels %>% select(label) %>% pull())
df2$name <- factor(df2$name,levels = hcdata$labels %>% select(label) %>% pull())
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")))
tree + heatmap+ plot_layout(widths = c(.3,1))、