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
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. > >-- View this message in context: http://www.nabble.com/Symbols-on-a-capscale-object-plot-tp19469679p19470027.html Sent from the R help mailing list archive at Nabble.com.
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" <mark_difford em yahoo.co.uk> > Sent: Saturday, September 13, 2008 9:21 AM > To: <r-help em 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 >>> 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 em 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. >>> >>> >> >> -- >> View this message in context: >> http://www.nabble.com/Symbols-on-a-capscale-object-plot-tp19469679p19470027.html >> Sent from the R help mailing list archive at Nabble.com. >> >> ______________________________________________ >> R-help em 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. >>