I've generated a plot of an RDA using R. When I add my biplot on to the RDA, it adds new axes that I would like to turn off. Here is some example data:
Site<-c(1,2,3,4,5,6)
inv1<-c(34,67,78,45,677,23)
inv2<-c(45,5,55,56,7,8)
inv3<-c(6,7,4,12,7,8)
depth<-c(3,1,6,7,10,57)
exampledata_exp<-data.frame(Site,depth)
exampledata_invs<-data.frame(inv1,inv2,inv3)
dpRDA.out<-capscale(exampledata_invs~depth+Site, data=exampledata_exp, distance="bray")
summary(dpRDA.out)
plot(dpRDA.out, display=c("sites"), type="n", scaling=1, cex=1, family="serif")#this is the way I want the plot borders to look
points(dpRDA.out, display = c("sites"))
points(dpRDA.out, display="bp", col="black", scaling=1, family="serif")
The last bit of code adds on a new axes. I have tried axes=FALSE, xaxt="n", axes(side=3, lwd=0). Any suggestions greatly appreciated.
libraries currently loaded:
library(vegan)
library(reshape)
library(ggplot2)
library(plyr)
library(MASS)
library(tables)
library(matrixStats)
You can switch off the new axes by setting the axis.bp parameter to FALSE in the last line. Try:
points(dpRDA.out, display="bp", col="black", scaling=1, family="serif", axis.bp = FALSE)