[R] Symbols on a capscale object plot

[Mark Difford]

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.
> 
> --------------------------------------------------
>> From: "Mark Difford" <mark_difford at yahoo.co.uk>
>> Sent: Saturday, September 13, 2008 9:21 AM
>> To: <r-help at 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
>>>>
>>>> ______________________________________________
>>>> 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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>>> View this message in context: 
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>>> Sent from the R help mailing list archive at Nabble.com.
>>>
>>> ______________________________________________
>>> 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.
>>>
> 
> ______________________________________________
> 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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