本地文件 s41564-021-00997-7.pdf

论文

Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen

今天的推文来重复一下论文中的figure3c 散点图添加拟合曲线

读取数据集

library(readxl)
df<-read_excel("41564_2021_997_MOESM10_ESM.xlsx")
head(df)
colnames(df)

最基本的散点图

library(ggplot2)
ggplot(data=df,aes(x=`mean Protection Score [a.u.]`,y=`mean Colonization [log10(CFU/mg)]`))+geom_point(aes(color=Phylum))+ggsave(filename = "fig3c.pdf",width = 6,height = 4,family="serif")

添加拟合曲线

ggplot(data=df,aes(x=`mean Protection Score [a.u.]`,y=`mean Colonization [log10(CFU/mg)]`))+geom_point(aes(color=Phylum))+geom_smooth(method = "lm",formula = "y~x",se=F,color="grey")+ggsave(filename = "fig3c.pdf",width = 6,height = 4,family="serif")

计算拟合方程的R和P值

df.lm<-lm(`mean Colonization [log10(CFU/mg)]`~`mean Protection Score [a.u.]`,data=df)
summary(df.lm)sqrt(0.242)ggplot(data=df,aes(x=`mean Protection Score [a.u.]`,y=`mean Colonization [log10(CFU/mg)]`))+geom_point(aes(color=Phylum))+geom_smooth(method = "lm",formula = "y~x",se=F,color="grey")+annotate(geom = "text",x=60,y=1.2,label=expression(italic(R)~"="~0.49~","~italic(P)~"="~5.4%*%10^-15),parse=T)+ggsave(filename = "fig3c.pdf",width = 6,height = 4,family="serif")

添加虚线注释框

ggplot(data=df,aes(x=`mean Protection Score [a.u.]`,y=`mean Colonization [log10(CFU/mg)]`))+geom_point(aes(color=Phylum))+geom_smooth(method = "lm",formula = "y~x",se=F,color="grey")+annotate(geom = "text",x=60,y=1.2,label=expression(italic(R)~"="~0.49~","~italic(P)~"="~5.4%*%10^-15),parse=T)+annotate(geom = "rect",xmin = 75,xmax = 100,ymin = 4.5,ymax = 7,alpha=0,color="black",lty="dashed")+ggsave(filename = "fig3c.pdf",width = 6,height = 4,family="serif")

最后是调节主题美化

colors<-c("#96d796","#aed75b","#599943","#499ef1","#f18282","#ffdf33")
ggplot(data=df,aes(x=`mean Protection Score [a.u.]`,y=`mean Colonization [log10(CFU/mg)]`))+geom_point(aes(fill=Phylum,color=Phylum),shape=21,key_glyph="rect")+geom_smooth(method = "lm",formula = "y~x",se=F,color="grey")+annotate(geom = "text",x=60,y=1.2,label=expression(italic(R)~"="~0.49~","~italic(P)~"="~5.4%*%10^-15),parse=T)+annotate(geom = "rect",xmin = 75,xmax = 100,ymin = 4.5,ymax = 7,alpha=0,color="black",lty="dashed")+theme_bw()+theme(panel.grid = element_blank(),legend.title = element_blank())+scale_fill_manual(values = colors)+scale_color_manual(values = colors)+ggsave(filename = "fig3c.pdf",width = 9.4,height = 4,family="serif")

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