Re: [R] Symbols on a capscale object plot

Sat, 13 Sep 2008 10:37:43 -0700 

Thank You Mark,
With your tip now I'm able to chance the sites names for real symbols. Well,
now I just have to find out how to change groups of sites names, that
compose a 'biofacies', with different symbols (actually six groups) in the
same plot.
Maybe if I can define a factor that specifies these groups and use this
factor to assign the symbols.
I don't know, I've to try, but I'm getting something, I hope.

Rodrigo.

--------------------------------------------------

From: "Mark Difford" <[EMAIL PROTECTED]>
Sent: Saturday, September 13, 2008 9:21 AM
To: <r-help@r-project.org>
Subject: Re: [R] 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
Laboratório de Micropaleontologia
Avenida Beira Mar s/n - CEP 83255-000
Pontal do Paraná - PR - BRASIL
Fone: (0**41) 3455-1496 ramal 217
Fax: (0**41) 3455-1105

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