被紅色框線圈住的散點圖

 

基礎繪圖函數箱線圖

有人留言說 和原圖不是很像，因為配色沒有按照論文中提供的代碼來。 下面是完全重復論文中的代碼

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)

 

• 讀入數據

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

• 最基本的散點圖

plot(rel_res~rel_crAss,data=HMP)

 

畫圖用plot()函數，需要指定畫圖用到的變量y和x，還有畫圖用到的數據data

原始代碼分別對 rel_res 和 rel_crAss取了log10

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

 

取log10以后可以看到散點分布的更加均勻了。

• 按照國家分組填充顏色

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)

 

• 更改點的大小

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

 

• 更改x軸和y軸的標簽

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)

 

• 更改坐標軸的范圍

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))

 

接下來將箱線圖和散點圖按照上下拼接到一起，用到的是par(fig=c(a,b,c,d)),這里需要滿足 a<b,c<d

具體可以參考鏈接 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)