被红色框线圈住的散点图

 

基础绘图函数箱线图

有人留言说 和原图不是很像，因为配色没有按照论文中提供的代码来。 下面是完全重复论文中的代码

cols <- c("#E69F00", "#56B4E9", "#009E73")
boxplot(log10(rel_crAss)~country,data=HMP,col=cols,
       axes=F,xlab=NULL,ylab=NULL,
       horizontal = T)
axis(2,at=c(1,2,3),labels=c("China", "Europe", "US"),las=1)
title("a",adj=0,line=0)

 

• 读入数据

HMP<-read.table("data/HMP.txt")

• 最基本的散点图

plot(rel_res~rel_crAss,data=HMP)

 

画图用plot()函数，需要指定画图用到的变量y和x，还有画图用到的数据data

原始代码分别对 rel_res 和 rel_crAss取了log10

plot(log10(rel_res)~log10(rel_crAss),data=HMP)

 

取log10以后可以看到散点分布的更加均匀了。

• 按照国家分组填充颜色

cols <- c("#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
plot(log10(rel_res)~log10(rel_crAss), data=HMP,
    bg=cols[as.factor(HMP$country)],pch=21)

 

• 更改点的大小

plot(log10(rel_res)~log10(rel_crAss), data=HMP,
    bg=cols[as.factor(HMP$country)],pch=21,cex=2)

 

• 更改x轴和y轴的标签

plot(log10(rel_res)~log10(rel_crAss), data=HMP, bg=cols[as.factor(HMP$country)], pch=21,
    ylab = "Normalized ARG abundance (log10)",
    xlab="Normalized crAssphage abundance (log10)", cex=2)

 

• 更改坐标轴的范围

plot(log10(rel_res)~log10(rel_crAss), data=HMP,
    bg=cols[as.factor(HMP$country)], pch=21,
    ylab = "Normalized ARG abundance (log10)",
    xlab="Normalized crAssphage abundance (log10)",
    cex=2,
    ylim=c(2.5, 4.5))

 

接下来将箱线图和散点图按照上下拼接到一起，用到的是par(fig=c(a,b,c,d)),这里需要满足 a

具体可以参考链接 https://blog.csdn.net/qingchongxinshuru/article/details/52004182

par(fig=c(0,1,0,0.75))
plot(log10(rel_res)~log10(rel_crAss), data=HMP,
    bg=cols[as.factor(HMP$country)], pch=21,
    ylab = "Normalized ARG abundance (log10)",
    xlab="Normalized crAssphage abundance (log10)",
    cex=2,
    ylim=c(2.5, 4.5))
par(fig=c(0,1,0.5,1),new=T)
boxplot(log10(rel_crAss)~country,data=HMP,col=cols,
       axes=F,xlab=NULL,ylab=NULL,
       horizontal = T)
axis(2,at=c(1,2,3),labels=c("China", "Europe", "US"),las=1)
title("a",adj=0,line=0)