Finally I got it.
I'm posting it here for people that need it in the future.
Bellow is the code that solved the issue.
Thank you so much Mark.
Without your help I'm not sure if I would be able to do that, at least not
in time!
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(Formula,dist="bray",add=T)
# Factor for the graphic groups (all sites numbered from 1 to 6, according
to the group it belongs)
FatoresRep<-read.xls('Fatores.xls',sheet=2,rowNames=T)
# Saving the capscale Scores in an object
ScoresdbRDA<-scores(dbRDA)
# The graphic
plot.cca(dbRDA,type='none',display=c('bp','sites'))
text.cca(dbRDA,dis='cn',col=323232,cex=0.7,lwd=2,lty='dotted')
points(ScoresdbRDA$sites[FatoresRep$Biofacies=='1',],pch=20)
points(ScoresdbRDA$sites[FatoresRep$Biofacies=='2',],pch=21)
points(ScoresdbRDA$sites[FatoresRep$Biofacies=='3',],pch=22,bg='gray')
points(ScoresdbRDA$sites[FatoresRep$Biofacies=='4',],pch=23,bg='gray')
points(ScoresdbRDA$sites[FatoresRep$Biofacies=='5',],pch=24)
points(ScoresdbRDA$sites[FatoresRep$Biofacies=='6',],pch=25,bg='black')
--------------------------------------------------
From: "Mark Difford" <[EMAIL PROTECTED]>
Sent: Saturday, September 13, 2008 4:10 PM
To: <r-help@r-project.org>
Subject: Re: [R] Symbols on a capscale object plot
Hi Rogrido,
Sorry: The first points() call was missing a vital comma. It should have
been.
points(ord.obj$scores[mydf$Site=="MarkerA", ], pch=21, bg="red")
See ?"["
Mark Difford wrote:
Hi Rodrigo,
Maybe if I can define a factor that specifies these groups and use this
factor to assign the symbols.
Yes, that's the idea. Some ordination-oriented packages make this easier
to do than others. You should look through vegan carefully to see the
full
offering. Nevertheless, it's pretty easy to do it from the ground up once
you get the knack.
You would do something like the following. Say you have a factor-column
called Site, the rows of which match the rows of the data frame (=mydf)
you used for the ordination. Then you could lasso your groups by doing:
points(ord.obj$scores[mydf$Site=="MarkerA"], pch=21, bg="red")
points(ord.obj$scores[1:10, ], pch=21, bg="red") ## by rownum()
HTH, Mark.
Rodrigo Aluizio wrote:
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.
--------------------------------------------------
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.
[[elided Yahoo spam]]
# 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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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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