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跟着Nature Plants学作图：R语言ggplot2画分组折线图并对坐标轴添加一些额外注释

2023-02-19 12:27:38 时间

论文

The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence

https://www.nature.com/articles/s41477-022-01146-6#Sec44

数据下载链接

https://doi.org/10.6084/m9.figshare.19125641

今天的推文重复一下论文中的Figure1b左上角的小图

image.png

今天推文的主要知识点是如何在绘图区域外添加一些文本和线段的注释，这里需要用到annotation_custom()函数

部分示例数据集

image.png

读取数据集 

library(readxl)

dat01<-read_excel("data/20220524/Nature_plant_fig1b.xlsx")
head(dat01)

指定列按照行来求平均值 

library(tidyverse)

dat01 %>% 
  mutate(new_col=rowMeans(.[,4:6])) -> new.dat

新构造一些数据用来添加绘图区域内的文本 

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"))

基本的分组折线图和添加文本 

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

在坐标轴区域添加注释

并对主题进行一些修改

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())

最终结果如下

image.png

说实话，额外注释的位置真不好搞，这些额外注释可能还是出图后借助其他软件来编辑比较合适

示例数据可以到论文中去下载，代码可以在推文中复制

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