r - 为什么我的地块的 0,0 参考线延伸到绘图区域之外？

Question

我在为我的 PCoA 图生成 R 中的图时遇到问题。由于某种原因，0,0 线延伸到绘图区域之外。任何帮助将不胜感激。

这是我的代码：

library(vegan)
library(ggfortify)
library(MASS)
options(max.print=100000)

rel.table.6_R$Covercrop_Presence<-as.factor(rel.table.6_R$Covercrop_Presence)
rel.table.6_R$Glyphosate_Application<-as.factor(rel.table.6_R$Glyphosate_Application)
rel.table.6_R$Timepoint<-as.factor(rel.table.6_R$Timepoint)
rel.table.6_R$Rep<-as.factor(rel.table.6_R$Rep)


Pot_id<- interaction(rel.table.6_R$Pot_No,rel.table.6_R$Rep,drop=TRUE)
data<- rel.table.6_R[,c(8:1340)]
colvec <- c("white","black")
colvec <- colvec[as.numeric(rel.table.6_R$Glyphosate_Application)]

colvecTP <- c("1","2","3","4","5")
colvecTP <- colvec[as.numeric(rel.table.6_R$Timepoint)]

shapes <- c(24, 21)
shapes <- shapes[as.numeric(rel.table.6_R$Covercrop_Presence)]
ld<-decostand(data,method="log",logbase=10)
ld_dist<-vegdist(ld,method="altGower")
data_dist<-vegdist(data,method="altGower")
data_distbray<-vegdist(data,method="bray")
nspecies<-dim(data)[2]

pdf("allplotsR2_ColorsFigs.pdf", 9, 7)

test.pco.bray<-capscale(data~1,distance="bray")

par(xpd = T, mar = par()$mar + c(0,0,0,9.5))
plot(test.pco.bray,type="none", main="PcoA PC1 vs PC2 Original Bray-Curtis", xlab="PC1 - XX.X % of variation explained",ylab="PC2 - XX.X % of variation explained")
points(test.pco.bray,choices=c(1,2),display="sites",bg= colvec,pch= shapes, cex=1.5)
#text(test.pco.l,choices=c(1,2),display="species",labels=c(1:nspecies))
with (test.pco.bray, legend(1.2, 1.05, c("Cover crop Glp+","Cover crop Glp-","Fallow Glp+","Fallow Glp-"), bty = "o", pch = c(24,24,21,21),pt.bg= c("black","white","black","white"),     cex=1.3,inset=0.01))
par(mar=c(5, 4, 4, 2) + 0.1)
dev.off()

这是我得到的结果：

标签： r