跟着BMC genomics学作图：R语言ggplot2+ggtree进化树拼接三角热图

library(ggtree)
library(treeio)
library(readxl)
library(ggplot2)
library(tidyverse)

library(patchwork)
library(see)

tree<-read.tree("sample.nwk")
tip.group<-read.csv("sample_group.csv")
tip.group
tree.a<-full_join(tree,tip.group,by="label")

as_tibble(tree.a) %>% 
  as.data.frame()

p1<-ggtree(tree.a,
       branch.length = "none",
       aes(color=group))+
  geom_tiplab(offset = 0.1)+
  theme(legend.position = "none")+
  scale_y_reverse()+
  scale_color_manual(values = c("#cc340c",
                                "#13a983",
                                "#3f60aa"),
                     na.value="black")
p1

df<-read_excel("example.xlsx")
df %>% pivot_longer(!sample,
                    names_to = "sample1",
                    values_to = "kaks") -> df1
df1$sample<-factor(df1$sample,
                   levels = rev(df$sample))
df1$sample1<-factor(df1$sample1,
                   levels = df$sample)
p2<-ggplot(data=na.omit(df1),aes(x=sample,y=sample1))+
  geom_tile(aes(fill=kaks),color="grey")+
  scale_fill_bluebrown_c()

p2

df1 %>% 
  filter(sample == sample1) -> df2

p2+
  geom_tile(data=df2,aes(x=sample,
                         y=sample1),
            fill="white",color="grey")+
  #theme_void() +
  theme(axis.text = element_text())-> p2.1

p2.2<-p2.1+theme(axis.title = element_blank(),
           axis.text.y = element_blank(),
           axis.ticks = element_blank(),
           panel.background = element_blank(),
           legend.position = c(0.9,0.8))
p2.2

p3<-ggtree(tree.a,
       branch.length = "none",
       aes(color=group))+
  #geom_tiplab()+
  theme(legend.position = "none")+
  #scale_y_reverse()+
  coord_flip()+
  scale_color_manual(values = c("#cc340c",
                                "#13a983",
                                "#3f60aa"),
                     na.value="black")
p3

(p1+xlim(0,8)+p2.2+
    plot_spacer()+p3)+
  plot_layout(ncol=2,
              widths = c(0.5,3),
              heights = c(3,0.5))