跟着Nature Genetics学作图：R语言ggplot2画图展示基因树的拓扑结构冲突

Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance
https://doi.org/10.1038/s41588-024-01683-0
今天的推文我们来复现一下论文中的 Fig2b

image.png
这里我的思路是画三条线段，用等腰三角形的三个顶点坐标来构造线段的起始和终止坐标，等腰三角形的三个顶点可以用函数polygon_regular()来获取，这个函数是用来构造多边形的顶点的，来自于gridExtra包。比如我要画一个等腰三角形
polygon_regular(n=3,phase = pi/2) %>%
as.data.frame() %>%
ggplot(aes(x=V1,y=V2))+
geom_polygon(fill=”#8092b2″,alpha=0.9)

image.png
加载需要用到的R包

library(gridExtra)
library(tidyverse)
library(ggplot2)
library(patchwork)
构造一个函数用来单个图

myfun<-function(linecolor,linewid, label.01,label.01.size, label.02,label.02.size, title.text, title.size){ polygon_regular(n=3) %>%
as.data.frame() %>%
head(n=3) -> dat
dat[3,] %>%
bind_cols(dat[1,] %>%
rename(“V3″=”V1”,
“V4″=”V2”)) -> dat01

dat[1,] %>%
bind_cols(dat[2,] %>%
rename(“V3″=”V1”,
“V4″=”V2”)) -> dat02

(dat[3,]/2 + dat[1,]/2) %>%
bind_cols((dat[3,]/2 + dat[2,]/2) %>%
rename(“V3″=”V1”,
“V4″=”V2”)) -> dat03
dat01 %>%
bind_rows(dat02) %>%
bind_rows(dat03) %>%
ggplot()+
geom_segment(aes(x=V1,xend=V3,y=V2,yend=V4),
linewidth=linewid,
color=linecolor,
lineend = “round”,
linejoin = “round”)+
theme_bw()+
theme(panel.grid = element_blank(),
axis.title = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
panel.border = element_rect(color=linecolor,linewidth=linewid))+
coord_equal()+
geom_text(data=dat[2,] %>%
bind_rows(dat[3,]/2 + dat[2,]/2) %>%
bind_rows(dat[3,]) %>%
mutate(label=label.01),
aes(x=V1,y=V2,label=label),
vjust=1.5,size=label.01.size)+
geom_text(data=data.frame(V1=c(dat[2,1],dat[3,1]),
V2=1,
label=label.02),
aes(x=V1,y=V2,label=label),
size=label.02.size,vjust=1,hjust=c(0,1))+
labs(title=title.text)+
theme(plot.title = element_text(hjust=0.5,size=title.size))+
xlim(-1,1)+
ylim(-1,1.2)

}
先画一个
myfun(linecolor = “#8092b2”,
linewid = 3,
label.01 = c(“H”,”B”,”C”),
label.01.size = 8,
label.02 = c(“Tree1″,”57%”),
label.02.size = 8,
title.text = “HBC lineage”,
title.size = 20) -> p1
p1

image.png
画9个然后拼图

myfun(linecolor = “#8092b2”,
linewid = 3,
label.01 = c(“H”,”B”,”C”),
label.01.size = 8,
label.02 = c(“Tree1″,”57%”),
label.02.size = 8,
title.text = “HBC lineage”,
title.size = 20) -> p1

myfun(linecolor = “#66b9a1”,
linewid = 3,
label.01 = c(“B”,”A”,”C”),
label.01.size = 8,
label.02 = c(“Tree1″,”48%”),
label.02.size = 8,
title.text = “ABC lineage”,
title.size = 20) -> p2

myfun(linecolor = “#dba134”,
linewid = 3,
label.01 = c(“B”,”D”,”C”),
label.01.size = 8,
label.02 = c(“Tree1″,”46%”),
label.02.size = 8,
title.text = “BCD lineage”,
title.size = 20) -> p3

myfun(linecolor = “#8092b2”,
linewid = 3,
label.01 = c(“B”,”H”,”C”),
label.01.size = 8,
label.02 = c(“Tree2″,”25%”),
label.02.size = 8,
title.text = NULL,
title.size = 20) -> p4

myfun(linecolor = “#8092b2”,
linewid = 3,
label.01 = c(“C”,”H”,”B”),
label.01.size = 8,
label.02 = c(“Tree3″,”18%”),
label.02.size = 8,
title.text = NULL,
title.size = 20) -> p7

myfun(linecolor = “#66b9a1”,
linewid = 3,
label.01 = c(“C”,”A”,”B”),
label.01.size = 8,
label.02 = c(“Tree2″,”28%”),
label.02.size = 8,
title.text = NULL,
title.size = 20) -> p5

myfun(linecolor = “#66b9a1”,
linewid = 3,
label.01 = c(“A”,”B”,”C”),
label.01.size = 8,
label.02 = c(“Tree3″,”24%”),
label.02.size = 8,
title.text = NULL,
title.size = 20) -> p8

myfun(linecolor = “#dba134”,
linewid = 3,
label.01 = c(“C”,”D”,”B”),
label.01.size = 8,
label.02 = c(“Tree2″,”31%”),
label.02.size = 8,
title.text = NULL,
title.size = 20) -> p6

myfun(linecolor = “#dba134”,
linewid = 3,
label.01 = c(“D”,”B”,”C”),
label.01.size = 8,
label.02 = c(“Tree3″,”23%”),
label.02.size = 8,
title.text = NULL,
title.size = 20) -> p9

wrap_plots(list(p1,p2,p3,p4,p5,
p6,p7,p8,p9))

image.png