Without data, I tried to reproduce your plot error:
plot(x=as.factor(2:8),y=2:8,xlim = c(1,10)
Which gives the following plot:
Changing your plot to:
boxplot(x= as.numeric(as.character(SS$Bed[XMSA=="MSSA"])), y= ACC[XMSA=="MSSA"] xlab="Bed",ylab="Growth", las=1, yaxt="n",ylim=c(1,5),xlim=c(1,10)) axis(2, at=c(1,2,3,4,5),labels=c("NG","SG","LG","MG","HG"),las=1)
Might solve your problem.
Edit
It seems that the formula changes to factors and orders it from 1 to the number of items, so I’ll use your trick on the y axis to solve this.
boxplot(ACC[XMSA=="MSSA"]~SS$Bed[XMSA=="MSSA"], xlab="Bed",ylab="Growth", las=1, yaxt="n",ylim=c(1,5),xlim=c(0,9),xaxt="n") axis(2, at=1:5,labels=c("NG","SG","LG","MG","HG"),las=1) axis(1, at=0:9,labels=1:10,las=1)
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