# R/plot.overly.R In dave: Functions for "Data Analysis in Vegetation Ecology"

#### Documented in plot.overly

```plot.overly<- function(x,...,colors=NULL,l.widths=NULL) {
o.overly<- x
tree<- o.overly\$tree
out<- pco(o.overly\$d.mat,k=2)
plot(out\$points[,1],out\$points[,2],xlab="PCOA axis 1",ylab="PCOA axis 2",asp=1,cex.axis=0.7,cex.lab=0.7,mgp=c(1.8,0.4,0))
abline(h=0,v=0,lwd=1.0,col="gray")
lines(tree,ord=out,display="sites",col="lightblue",lwd=1.5)    # minimum spanning tree in ordination
pos.corr<-c(3,1,1,1,3,1,2,3,3,3,3,3,3,3,4,3,2,2,1,4,3,3,3,3,3,3,3,4,3,3,3,
3,3,3,4,3,3,3,2,3,3,2,3,3,3,4,3,3,3,2,2,3,3,4,3,2,4,3,3)
text(out\$points[,1],out\$points[,2],o.overly\$plot.labels,pos=pos.corr,cex=0.6)
#
# plot of alignment of time series
# --------------------------------
veg<- o.overly\$vegraw
nspec<- ncol(veg)
nt<- ncol(o.overly\$d.mat)
range<- o.overly\$n.tsteps
plot(c(0,range*1.05),c(0,nt),type="n",xlab="Time step no.",ylab="Time series",cex.lab=0.7)
for (i in 1:nt) {
lines(c(o.overly\$linex1[i],o.overly\$linex2[i]),c(i,i),lwd=2.5,col="gray")
text(o.overly\$linex2[i],i,o.overly\$ltext[i],pos=4,cex=0.6)
}
abline(v=0,lwd=1.0,col="gray")
#
# plot of final time series
# -------------------------
# The next 2 lines set defaults if linewidths are null
#  nlines<- dim(o.overly\$vegraw)[2]
defwidth<- is.null(l.widths)
if(defwidth == TRUE) ll.widths<- seq(0.5,4.0,0.5)
if(defwidth != TRUE) ll.widths<- l.widths
# The same now with colors
defcol<- is.null(colors)
if(defcol == TRUE) c.colors<- c("darkred","red1","darkorange","gold","lightgreen","darkolivegreen4")
if(defcol != TRUE) c.colors<- colors
#
sint<- o.overly\$sint
M<- o.overly\$tser.data
vegtypes<- o.overly\$vegtypes
timescal<- seq(0,(range-1)*sint,sint)
par(mfrow=c(1,1),omi=c(2,0,0,0))
plot(c(0,range*sint),c(0,max(M)),xlab="Time units",ylab="Cover scale",type="n")
for(i in 1:nspec) lines(timescal,M[,i],col=c.colors[i],lwd=ll.widths[i],lty=1)
legend("topleft",vegtypes,lty=1,lwd=ll.widths,col=c.colors,ncol=2,bty="n",cex=0.8,text.font=3)
}
```

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dave documentation built on Nov. 17, 2017, 7:45 a.m.