Symbols on a capscale object plot
Hi Rodrigo,
I would like to use something like squares, triangles and circles (filled and empty).
You would normally add this using points(): ?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()
___________________________________ MSc. Rodrigo Aluizio Centro de Estudos do Mar/UFPR Laborat?rio de Micropaleontologia Avenida Beira Mar s/n - CEP 83255-000 Pontal do Paran? - PR - BRASIL Fone: (0**41) 3455-1496 ramal 217 Fax: (0**41) 3455-1105 ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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