跟着Nature Communications学作图：R语言ggplot2画流程图
跟着Nature Communications学作图：R语言ggplot2画流程图
论文
A highly conserved core bacterial microbiota with nitrogen-fixation capacity inhabits the xylem sap in maize plants
https://www.nature.com/articles/s41467-022-31113-w
本地pdf s41467-022-31113-w.pdf
数据代码链接
https://github.com/PlantNutrition/Liyu
今天的推文我们来复现一下论文中的Figure2B，论文里没有提供这个图的代码，可以尝试用ggplot2模仿一下
image.png
当然这个图用ppt很容易实现。用ggplot2来做会稍微繁琐一点，但是后续多图组合会方便很多
流程图就是文本和箭头的组合，可以借助geom_text()函数和geom_segment()函数来做
首先是文本标签
library(ggplot2)
ggplot()+
geom_label(aes(x=0,y=0),label=" VE ",
color="white",
fontface="bold",
fill="#547e34",
size=5,
label.size = 0)
image.png
这里有个问题是背景颜色条和文本的宽度是一致的，如何单独调整背景的颜色条的宽度暂时想不到办法了，我的办法是给文本前后加空格
https://stackoverflow.com/questions/48195587/how-to-set-a-standard-label-size-in-ggplots-geom-label
这个链接里重新自己定义了一个函数，关于自己写ggplot2的绘图函数我还看不明白
添加箭头
ggplot()+
geom_label(aes(x=0,y=0),label=" VE ",
color="white",
fontface="bold",
fill="#547e34",
size=5,
label.size = 0)+
geom_label(aes(x=1,y=0),label=" SE ",
color="white",
fontface="bold",
fill="#547e34",
size=5,
label.size = 0)+
geom_label(aes(x=0.5,y=1),label=" LE ",
color="white",
fontface="bold",
fill="#a4c98a",
size=5,
label.size = 0)+
geom_label(aes(x=0.5,y=2),label=" P ",
color="white",
fontface="bold",
fill="#a4c98a",
size=5,
label.size = 0)+
geom_label(aes(x=0.5,y=-1),label=" RE ",
color="white",
fontface="bold",
fill="#b9860c",
size=5,
label.size = 0)+
geom_label(aes(x=-0.4,y=-1),label=" RS ",
color="white",
fontface="bold",
fill="#8b814b",
size=5,
label.size = 0)+
geom_label(aes(x=-1.2,y=-1),label=" BS ",
color="white",
fontface="bold",
fill="#8b814b",
size=5,
label.size = 0)+
xlim(-1.5,1.5)+
ylim(-1.5,2.2)+
geom_segment(aes(x=0.2,xend=0.8,y=0.05,yend=0.05),
arrow = arrow(angle=30,type = "closed",
length = unit(3,'mm')),
color="#516896")+
geom_segment(aes(x=0.8,xend=0.2,y=-0.05,yend=-0.05),
arrow = arrow(angle=30,type = "closed",
length = unit(3,'mm')),
color="#516896")+
geom_segment(aes(x=0,xend=0.5,y=0.1,yend=0.9),
arrow = arrow(angle=30,type = "closed",
length = unit(3,'mm')),
color="#516896")+
geom_segment(aes(x=0.4,xend=-0.1,y=0.9,yend=0.1),
arrow = arrow(angle=30,type = "closed",
length = unit(3,'mm')),
color="#516896")+
geom_segment(aes(x=1.1,xend=0.6,y=0.1,yend=0.9),
arrow = arrow(angle=30,type = "closed",
length = unit(3,'mm')),
color="#516896")+
geom_segment(aes(x=0.5,xend=1,y=0.9,yend=0.1),
arrow = arrow(angle=30,type = "closed",
length = unit(3,'mm')),
color="#516896") -> p1
p1
image.png
https://cran.r-project.org/web/packages/ggarchery/readme/README.html
添加箭头有一个专门的R包
这样一个一个添加太麻烦，可以把数据整理好
new.dat.01<-data.frame(
x= c(0,0.4,1,0.5,0.5,-1.2,-1,-0.2),
xend=c(0.5,-0.1,0.6,0.9,0.5,0.3,-0.6,0.3),
y =c(-0.1,-0.9,-0.1,-0.9,1.9,2,-1,-1),
yend=c(-0.9,-0.1,-0.9,-0.1,1.1,2,-1,-1))
p1 +
geom_segment(data=new.dat.01,
aes(x=x,xend=xend,y=y,yend=yend),
arrow = arrow(angle=30,type = "closed",
length = unit(3,'mm')),
color="#516896")+
geom_segment(aes(x=-1.2,xend=-1.2,y=-0.9,yend=2),
color="#516896")-> p2
p2
image.png
添加数字文本
new.data.02<-data.frame(
x=c(-0.8,0,-0.5,0.7,-0.9,0.3,1.1,0.5),
y=c(-0.9,-0.9,2.1,1.5,0.5,0.3,0.4,0.5),
label=c(93.68,60.61,63.53,88.84,27.06,9.15,1.91,45.61)
)
p2 +
geom_text(data = new.data.02,
aes(x=x,y=y,label=paste0(label,"%"))) -> p3
p3
image.png
拼图
library(patchwork)
p2 +
p3+ theme_void()
image.png
结论
好像确实有点繁琐，如果是真实数据不如直接用ppt画，然后借助其他软件拼图划算。如果是学习ggplot2可以尝试
数据和代码直接在推文里复制就可以，如果是学习ggplot2可以自己亲自敲一遍试试