uRDA <- function(otutab,env = NULL, mySite=NULL, scale=FALSE, biplot=FALSE, choices=1:2, display = "sites",
showsp=TRUE, legPos ="bottomright",saveplot=FALSE, ...){
obj <- rda(otutab, scale = scale)
print(summary(obj))
axes = paste0("PC", choices)
xlbl = paste(axes[1], getpropX(obj, choices))
ylbl = paste(axes[2], getpropY(obj, choices))
pchx = pchChoose(mySite)
my.col = colChoose(mySite)
if(is.null(mySite)) {my.site = as.factor(rep("site", nrow(otutab)))
legends = FALSE
} else { my.site = mySite
legends= TRUE}
if(biplot){
biplot(obj, scaling = 3, choices = choices, type = c("text", "points"), cex.lab=1.5,cex.axis=1.2,
main = "Unconstrained PCA biplot - scaling 3")
if(legends){
legs = levels(mySite)
ncols = ncolegend(mySite)
yspace = yinterspace(mySite)
legend(legPos, legend = legs, bty="o", cex=1.5, pch= pchx,
col=my.col, ncol = ncols, y.intersp = yspace)
}
if(saveplot){
dev.copy2pdf(file = paste0("Unconstained_RDA_plot_",deparse(substitute(otutab)),".pdf"),
useDingbats = FALSE)
}
} else {
plot(obj,type="n",xlab = xlbl, ylab = ylbl, cex.lab = 1.5, cex.axis=1.2, choices=choices,
main = paste("Unconstrained RDA plot for", deparse(substitute(otutab))))
abline(h=0,v=0,lty="dashed",col="grey")
points(obj, display="si",cex=1.2,pch= pchx[my.site], choices = choices,
col=my.col[my.site], bg=my.col[my.site], ...)
text(obj,display="si", choices = choices, cex=0.9,col=my.col[my.site],adj=-0.1, ...)
if(showsp){
points(obj, display="sp", choices = choices, cex=0.8, pch= '+', col='red')
text(obj, display="sp", choices = choices, cex=0.9, col = my.col[my.site],adj=-0.1)
}
if(legends){
legs = levels(mySite)
ncols = ncolegend(mySite)
yspace = yinterspace(mySite)
legend(legPos, legend = legs, bty="o", cex=1.5, pch= pchx,
col=my.col, ncol = ncols, y.intersp = yspace)
}
if(saveplot)
dev.copy2pdf(file = paste0("Unconstained_RDA_plot_",deparse(substitute(otutab)),".pdf"),useDingbats =F)
}
}
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