[R] Mirror Image on Biplot Graphic

Mark Difford mark_difford at yahoo.co.uk
Tue Oct 7 20:43:04 CEST 2008 

Hi Rodrigo,

I looked through my scripts and found my old hack. __WARNING__: Be very
careful to check that
the mirror isn't broken and that all is in order! Make sure that you are
reversing the axes you want. In your original post you mention axis 2, i.e.
y-axis. Below you have used axis 1.

## This does axis 2
mynew.cca <- my.cca
for (i in 2:8) mynew.cca$CCA[[i]][, 2] <- mynew,cca$CCA[[i]][, 2] * -1

plot(mynew.cca)

## This does axis 1
for (i in 2:8) mynew.cca$CCA[[i]][, 1] <- mynew,cca$CCA[[i]][, 1] * -1

Regards, Mark.


Rodrigo Aluizio wrote:
> 
> 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$biplot),col=323232,cex=0.6,lwd=2,lty='dotted')
> Doesn't return an error, but it's not a mirror image as expected, it's 
> nonsense.
> 
> --------------------------------------------------
> From: "Mark Difford" <mark_difford at yahoo.co.uk>
> Sent: Tuesday, October 07, 2008 12:22 PM
> To: <r-help at r-project.org>
> Subject: Re: [R] Mirror Image on Biplot Graphic
> 
>>
>> Hi Rodrigo,
>>
>> Sorry again: the structure vegan uses is quite complex. Technically you
>> should use the extractor function scores() to extract what you want from 
>> the
>> object, e.g. scores(my.cca, display="species") or scores(my.cca,
>> display="cn") [centroids]. I did work out a quicker way of reversing
>> axes,
>> but that seems to have gone walking...and I am not using vegan at the
>> moment.
>>
>> Quickest hack is to make a copy of the objects you want to plot,
>> reversing
>> orientations along the way. So do (my.cca is your original object):
>>
>> Temp.data <- scores(my.cca, display=c("sites", "species", "cn"))
>>
>> ## Reverse yaxes
>> Temp.data$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)$sites[,2]*-1
>>>>
>>>> Any ideas? I'm trying similar things but without success.
>>>>
>>>> --------------------------------------------------
> 
>>>> Sent: Tuesday, October 07, 2008 10:34 AM
>>>> To: <r-help at r-project.org>
>>>> Subject: Re: [R] Mirror Image on Biplot Graphic
>>>>
>>>>>
>>>>> Hi Rodrigo,
>>>>>
>>>>> Sorry, that will not return a result (I use several different 
>>>>> ordination
>>>>> packages, in most of which this is possible). What you need to do with
>>>>> vegan
>>>>> is the following:
>>>>>
>>>>> scores(mynew.cca)$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 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/Mirror-Image-on-Biplot-Graphic-tp19857549p19858268.html
>>>>> 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.
>>>
>>>
>>
>> -- 
>> 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 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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