[R] Mirror Image on Biplot Graphic
Rodrigo Aluizio
r.aluizio at gmail.com
Tue Oct 7 19:33:22 CEST 2008
Ok Mark, it worked for the species.
I still get an error if I try with biplot (cn,sp), but it's not a problem,
repositioning the species is enough.
Thanks once again.
Just for future consults the error that still remains:
CAPpotiFTI<-scores(CAPpotiFT, display=c('bp','species','cn','sites')
CAPpotiFTI$species[,1]<-CAPpotiFTI$species[,1]*-1
CAPpotiFTI$cn[,1]<-CAPpotiFTI$cn[,1]*-1
CAPpotiFTI$sites[,1]<-CAPpotiFTI$sites[,1]*-1
CAPpotiFTI$bp[,1]<-CAPpotiFTI$bp[,1]*-1
plot.cca(CAPpotiFTI,type='none',display=c('bp','species'),main='Total Fauna
+ Species x Environment')
Erro em match.arg(display) : 'arg' must be of length 1
or
text.cca(scores(CAPpotiFTI$biplot),col=323232,cex=0.6,lwd=2,lty='dotted')
Doesn't return an error, but it's not a mirror image as expected, it's
nonsense.
--------------------------------------------------
From: "Mark Difford" <mark_difford em yahoo.co.uk>
Sent: Tuesday, October 07, 2008 12:22 PM
To: <r-help em r-project.org>
Subject: Re: [R] Mirror Image on Biplot Graphic
>
> Hi Rodrigo,
>
> Sorry again: the structure vegan uses is quite complex. Technically you
> should use the extractor function scores() to extract what you want from
> the
> object, e.g. scores(my.cca, display="species") or scores(my.cca,
> display="cn") [centroids]. I did work out a quicker way of reversing axes,
> but that seems to have gone walking...and I am not using vegan at the
> moment.
>
> Quickest hack is to make a copy of the objects you want to plot, reversing
> orientations along the way. So do (my.cca is your original object):
>
> Temp.data <- scores(my.cca, display=c("sites", "species", "cn"))
>
> ## Reverse yaxes
> Temp.data$sites[, 2] <- Temp.data$sites[, 2] * -1
> Temp.data$species[, 2] <- Temp.data$species[, 2] * -1
> Temp.data$centroid[, 2] <- Temp.data$centroid[, 2] * -1
>
> Do this for all the things you are plotting whose axes you want reversed.
> Check this against your original plot to ensure that the mirror isn't
> broken.
>
> You can then use the Temp.data with the scores() function to make your
> plot.
>
> ## Mock e.g.
> points(scores(Temp.data, display="sites"), pch=21)
>
> Regards, Mark.
>
>
> Rodrigo Aluizio wrote:
>>
>>> Thanks a lot for your help (again) Mark.
>>> I adapted your suggestion to my analysis.
>>> But I'm getting and error when trying to apply the new values.
>>> The error is:
>>>
>>> Erro em scores(CAPpotiFTI)$species[, 2] <- scores(CAPpotiFTI)$species[,
>>> :
>>> não foi posssível encontrar a função "scores<-"
>>>
>>> Translating:
>>> Error at scores(CAPpotiFTI)$species[, 2] <- scores(CAPpotiFTI)$species[,
>>> :
>>> it's not possible to find the function "scores<-"
>>>
>>> Bellow how I applied the suggestion:
>>> CAPpotiFTI<-CAPpotiFT
>>> scores(CAPpotiFTI)$species[,2]<-scores(CAPpotiFTI)$species[,2]*-1
>>> scores(CAPpotiFTI)$sites[,2]<-scores(CAPpotiFTI)$sites[,2]*-1
>>>
>>> Any ideas? I'm trying similar things but without success.
>>>
>>> --------------------------------------------------
>>> Sent: Tuesday, October 07, 2008 10:34 AM
>>> To: <r-help em r-project.org>
>>> Subject: Re: [R] Mirror Image on Biplot Graphic
>>>
>>>>
>>>> Hi Rodrigo,
>>>>
>>>> Sorry, that will not return a result (I use several different
>>>> ordination
>>>> packages, in most of which this is possible). What you need to do with
>>>> vegan
>>>> is the following:
>>>>
>>>> scores(mynew.cca)$species[, 2] <- scores(mynew.cca)$species[, 2] * -1
>>>>
>>>> You will be able to do the rest.
>>>>
>>>> Regards, Mark.
>>>>
>>>>
>>>> Mark Difford wrote:
>>>>>
>>>>> Hi Rodrigo,
>>>>>
>>>>>>> I need to rotate on y axis the lines and symbols of constrained and
>>>>>>> sites representation.
>>>>>
>>>>> Easiest is to multiply the axis you want to invert by -1. Something
>>>>> like
>>>>> the following, where my.cca is the orginal object and yax = obj[, 2]
>>>>> (xax
>>>>> being obj[, 1]). Obviously, copying isn't necessary.
>>>>>
>>>>> mynew.cca <- my.cca
>>>>> mynew.cca$scores$species[, 2] <- my.cca$scores$species[, 2] * -1
>>>>> mynew.cca$scores$sites[, 2] <- my.cca$scores$sites[, 2] * -1
>>>>> mynew.cca$scores$centroids[, 2] <- my.cca$scores$centroids[, 2] * -1
>>>>>
>>>>> Regards, Mark.
>>>>>
>>>>>
>>>>> Rodrigo Aluizio wrote:
>>>>>>
>>>>>> He everybody,
>>>>>> Well I have a biplot CCA-like origined from plot.cca (vegan package).
>>>>>> I
>>>>>> need to rotate on y axis the lines and symbols of constrained and
>>>>>> sites
>>>>>> representation. If I do that on an image editor, I rotate everything,
>>>>>> including titles, axes labels and positions. I just need to rotate
>>>>>> the
>>>>>> inner par and keep the variables names (constrained) and symbols in
>>>>>> the
>>>>>> new positions but with the right direction.
>>>>>> So, is there on R a way to do that while creating the image?
>>>>>> Here is the code that generate the graphic.
>>>>>>
>>>>>> plot.cca(CAPpotiFT,type='none',display=c('bp','sites'),main='Total
>>>>>> Fauna
>>>>>> Sites x Environment')
>>>>>> text.cca(CAPpotiFT,dis='cn',col='black',cex=0.6,lwd=0.5,lty='dotted')
>>>>>> points(ScoresCAPFT$sites[FatoresRep$BiofaciesBC=='1',],pch=21)
>>>>>> points(ScoresCAPFT$sites[FatoresRep$BiofaciesBC=='2',],pch=20)
>>>>>> points(ScoresCAPFT$sites[FatoresRep$BiofaciesBC=='3',],pch=22,bg='gray')
>>>>>> points(ScoresCAPFT$sites[FatoresRep$BiofaciesBC=='4',],pch=24)
>>>>>> points(ScoresCAPFT$sites[FatoresRep$BiofaciesBC=='5',],pch=24,bg='black')
>>>>>> points(ScoresCAPFT$sites[FatoresRep$BiofaciesBC=='6',],pch=25,bg='gray')
>>>>>>
>>>>>> Thanks in advice.
>>>>>> ___________________________________
>>>>>> MSc. Rodrigo Aluizio
>>>>>> Centro de Estudos do Mar/UFPR
>>>>>> Laboratório de Micropaleontologia
>>>>>>
>>>>>> [[alternative HTML version deleted]]
>>>>>>
>>>>>>
>>>>>> ______________________________________________
>>>>>> 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/Mirror-Image-on-Biplot-Graphic-tp19857549p19858268.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/Mirror-Image-on-Biplot-Graphic-tp19857549p19860594.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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