Creating your own biplot for ordinations (e.g. ecological matrices with environmental data) isn't that hard - hardest part is figuring out how to get zero to line-up

myBiPlot.R

# x is the score for the horizontal axis, xx is the loading for that axis
# y is the score for the vertical axis, yy is the loading for that axis
# and the labels for each can also be set

myBiPlot<-function(x,y,xx,yy
		,xlab="",ylab=""
		,xxlab="",yylab=""){
	oldPar<-par(no.readonly=TRUE)
	par(mar=c(5,5,5,5))
	#
	rangeBalance<-function(data){
		range<-range(c(0,data))
		range/diff(range)
		}
	#
	balanceX<-rangeBalance(xx)*diff(range(c(0,x)))
	balanceXX<-rangeBalance(x)*diff(range(c(0,xx)))
	rangeX<-extendrange(c(x,balanceX,0))
	rangeXX<-extendrange(c(xx,balanceXX,0))
	#
	balanceY<-rangeBalance(yy)*diff(range(c(0,y)))
	balanceYY<-rangeBalance(y)*diff(range(c(0,yy)))
	rangeY<-extendrange(c(y,balanceY,0))
	rangeYY<-extendrange(c(yy,balanceYY,0))
	#
	plot(x,y
		,xlim=rangeX
		,ylim=rangeY
		,xlab=xlab
		,ylab=ylab)
	par(new=TRUE)
	plot(xx,yy,type="n",
		,xlim=rangeXX
		,ylim=rangeYY
		,xlab="",ylab=""
		,xaxt="n",yaxt="n")
	axis(3);axis(4)
	mtext(xxlab,side=3,line=3)
	mtext(yylab,side=4,line=3)
	arrows(x0=0,y0=0,
		length=0.1,
		x1=xx,y1=yy)	
	par(oldPar)
	}

# an example

set.seed(1)
x<-rnorm(20)*10
y<-rnorm(20)*10
xx<-rnorm(4)
yy<-rnorm(4)+1


myBiPlot(x=x,y=y,xx=xx,yy=yy,
	xlab="X Scores",ylab="Y Scores",
	xxlab="X Loadings",yylab="Y Loadings")