論文
The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence
https://www.nature.com/articles/s41477-022-01146-6#Sec44
數(shù)據(jù)下載鏈接
https://doi.org/10.6084/m9.figshare.19125641
今天的推文重復(fù)一下論文中的Figure1b左上角的小圖
image.png
今天推文的主要知識(shí)點(diǎn)是如何在繪圖區(qū)域外添加一些文本和線段的注釋，這里需要用到annotation_custom()函數(shù)
部分示例數(shù)據(jù)集
image.png
讀取數(shù)據(jù)集
library(readxl)
dat01<-read_excel("data/20220524/Nature_plant_fig1b.xlsx")
head(dat01)
指定列按照行來(lái)求平均值
library(tidyverse)
dat01 %>%
mutate(new_col=rowMeans(.[,4:6])) -> new.dat
新構(gòu)造一些數(shù)據(jù)用來(lái)添加繪圖區(qū)域內(nèi)的文本
dftext<-data.frame(x=c(150,150,150,112.5),
y=c(15,70,95,20)/100,
label=c("0.03","66.83","88.97","Centromere"))
基本的分組折線圖和添加文本
library(ggplot2)
ggplot()+
geom_line(data=new.dat,aes(x=Window,y=new_col,color=Context),
size=2)+
geom_vline(xintercept = 100,lty="dashed",
color="red",
size=1)+
geom_vline(xintercept = 125,lty="dashed",
color="red",
size=1)+
geom_text(data=dftext,aes(x=x,y=y,label=label))
image.png
在坐標(biāo)軸區(qū)域添加注釋
并對(duì)主題進(jìn)行一些修改
library(grid)
ggplot()+
geom_line(data=new.dat,aes(x=Window,y=new_col,color=Context),
size=2)+
geom_vline(xintercept = 100,lty="dashed",
color="red",
size=1)+
geom_vline(xintercept = 125,lty="dashed",
color="red",
size=1)+
geom_text(data=dftext,aes(x=x,y=y,label=label))+
coord_cartesian(clip = "off")+
annotation_custom(grob = linesGrob(gp=gpar(col="#e9d3ff",
lwd=8,
lineend="square")),
xmin=0,xmax=100,
ymin=-0.08,
ymax=-0.08)+
annotation_custom(grob = linesGrob(gp=gpar(col="#e9d3ff",
lwd=8,
lineend="square")),
xmin=125,xmax=225,
ymin=-0.08,
ymax=-0.08)+
annotation_custom(grob = linesGrob(gp=gpar(col="#f7931e",
lwd=8,
lineend="square")),
xmin=0,xmax=1,
ymin=-0.08,
ymax=-0.08)+
annotation_custom(grob = linesGrob(gp=gpar(col="#93278f",
lwd=8,
lineend="square")),
xmin=99,xmax=100,
ymin=-0.08,
ymax=-0.08)+
annotation_custom(grob = linesGrob(gp=gpar(col="#93278f",
lwd=8,
lineend="square")),
xmin=124,xmax=125,
ymin=-0.08,
ymax=-0.08)+
annotation_custom(grob = linesGrob(gp=gpar(col="#f7931e",
lwd=8,
lineend="square")),
xmin=224,xmax=225,
ymin=-0.08,
ymax=-0.08)+
annotation_custom(grob = pointsGrob(pch=19,
size=unit(0.8,'char')),
xmin=112.5,ymin=-0.08,
xmax=112.5,ymax=-0.08)+
annotation_custom(grob = segmentsGrob(gp=gpar(col="black",
lwd=2,
lineend="square"),
arrow = arrow()),
xmin=112.5,
ymin=0.125,
xmax=112.5,
ymax=-0.02)+
annotation_custom(grob = segmentsGrob(gp=gpar(col="black",
lwd=2,
lineend="square"),
arrow = arrow(angle=20,
length = unit(2,'mm'))),
xmin=100,
ymin=-0.2,
xmax=100,
ymax=-0.08)+
annotation_custom(grob = segmentsGrob(gp=gpar(col="black",
lwd=2,
lineend="square"),
arrow = arrow(angle=20,
length = unit(2,'mm'))),
xmin=125,
ymin=-0.2,
xmax=125,
ymax=-0.08)+
annotation_custom(grob = textGrob(label = "Pericentromeric regions",
just = "top",
hjust=0.5),
xmin=112.5,
ymin=-0.2,
xmax=112.5,
ymax=-0.2)+
annotation_custom(grob = segmentsGrob(gp=gpar(col="black",
lwd=2,
lineend="square"),
arrow = arrow(angle=20,
length = unit(2,'mm'))),
xmin=225,
ymin=-0.2,
xmax=225,
ymax=-0.08)+
annotation_custom(grob = textGrob(label = "Teloere",
just = "top",
hjust=0.5),
xmin=225,
ymin=-0.2,
xmax=225,
ymax=-0.2)+
scale_y_continuous(limits = c(0,1),
breaks = seq(0,1,0.25),
labels = seq(0,1,0.25)*100)+
scale_color_manual(values = c("#66c2a5","#fc8d62","#8da0cb"))+
labs(x="",y="Methylation level (%)")+
theme_bw()+
theme(axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
plot.margin = unit(c(0.1,0.1,2,0.1),'cm'),
panel.grid = element_blank())
最終結(jié)果如下
image.png
說(shuō)實(shí)話，額外注釋的位置真不好搞，這些額外注釋可能還是出圖后借助其他軟件來(lái)編輯比較合適
示例數(shù)據(jù)可以到論文中去下載，代碼可以在推文中復(fù)制，或者給推文打賞一元獲取我整理好的數(shù)據(jù)和代碼
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