[R] Symbols on a capscale object plot

Rodrigo Aluizio r.aluizio at gmail.com
Sat Sep 13 23:44:16 CEST 2008


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" <mark_difford em yahoo.co.uk>
Sent: Saturday, September 13, 2008 4:10 PM
To: <r-help em 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 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.
>>>>>>
[[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
>>>>>>
>>>>>> ______________________________________________
>>>>>> 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.
>>>>>
>>>
>>> ______________________________________________
>>> 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-tp19469679p19473735.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.
>



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