[R] Symbols on a capscale object plot

Mark Difford mark_difford at yahoo.co.uk
Sat Sep 13 14:21:01 CEST 2008

Hi Rodrigo,

>> I would like to use something like squares, triangles and circles (filled
>> and empty).

You would normally add this using points():

plot(1:10, type="n")
points(1:5, pch=21:25, bg=1:5)
points(6:10, pch=21:25, bg=c(1,"darkgrey","cyan", "bisque"))
points(6:10, y=rep(6,5), pch=1:5)

I don't know what vegan is doing at the moment but there used to be a points
command for doing this (sub ordiplot, I think). Vegan mostly still uses base
graphics so you can always get your scores [via: scores(ord.object): see
?scores] from your saved ordination object and add them as per above.

Regards, Mark.

Rodrigo Aluizio wrote:
> Hi, I'm a beginner with R, but I'm getting excellent results with it.
> Well I've got an capscale object (vegan package) and I want to made a
> biplot
> with symbols representing six groups of areas.
> With the plot.cca function and some par attributes (like 'labels') I was
> able to substitute the samples names for keyboard symbols
> ('x','o','#',ect),
> but it's far from the ideal.
> I've already search about it and find something using 'Hershey' fonts
> symbols for a scatterplot, but it didn't work for the biplot (capscale
> object).
> I would like to use something like squares, triangles and circles (filled
> and empty).
> Does anyone have and idea to solve it?
> Thank you for your attention and patience
> Sorry if the English is not that good, I'm Brazilian.
> Here is the script I'm using!
> # The analysis
> library(vegan)
> library(xlsReadWrite)
> PotiAbio<-read.xls('PotiAbioCanoco.xls',sheet=1,rowNames=T)
> PotiBio<-read.xls('FatorialReplica.xls',sheet=8,rowNames=T)
> attach(PotiAbio)
> LogPotiBio<-log(PotiBio+1)
> dbRDA<-capscale(t(LogPotiBio)~"Environmental Variables",dist="bray",add=T)
> dbRDA
> #Preparing to generate and save the graphic
> SymbolsRep<-read.xls('Fatores.xls',sheet=2)
> tiff('dbRDAPontos.tif',width=1250,height=1250,res=150)
> plot.cca(dbRDA,type='none',display=c('bp','sites'))
> text.cca(dbRDA,dis='cn',col=323232,cex=0.7,lwd=2,lty='dotted')
> text.cca(dbRDA,dis='sites',col='black',cex=0.8,labels=FatoresSymbols$RepSimb)
> dev.off()
> ___________________________________
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> Centro de Estudos do Mar/UFPR
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