[R] Mirror Image on Biplot Graphic
Mark Difford
mark_difford at yahoo.co.uk
Tue Oct 7 22:17:33 CEST 2008
Hi Rodrigo,
Yes it does, but this will work. You have erroneously used a "," in your
call, it should be a ".", if anything. You have also inserted "cca"... And
the axes being switched must be conformant:
>> CAPpotiFTI<-CAPpotiFT
>> for(i in c(2:8,15))
>> CAPpotiFTI$CCA[[i]][,2]<-CAPpotiFTI,cca$CCA[[i]][,1]*-1 ## you are
>> writing axis 1 over axis 2; and there is no "...,cca..."
>>>>>>>>>>>>>Erro: unexpected ',' in "for(i in c(2:8,15)) ## unexpected
comma
>> CAPpotiFTI$CCA[[i]][,2]<-CAPpotiFTI,"
## Using your example to switch axis 1. Make sure that CAPpotiFT exists and
is your
## original object. Copy and paste the lines below into your R console
window and run
CAPpotiFTI <- CAPpotiFT
for(i in c(2:8,15)) CAPpotiFTI$CCA[[i]][, 1]<-CAPpotiFTI$CCA[[i]][, 1] * -1
Cheers, Mark.
Rodrigo Aluizio wrote:
>
> Sorry for the mistake, I'm trying to rotate the CAP 1 axis not 2!
> Ah well, I tried the this other way, but it gave me an error.
> Something in the syntax, I tried to change something but didn't fix the
> error.
>
> CAPpotiFTI<-CAPpotiFT
> for(i in c(2:8,15))
> CAPpotiFTI$CCA[[i]][,2]<-CAPpotiFTI,cca$CCA[[i]][,1]*-1
> Erro: unexpected ',' in "for(i in c(2:8,15))
> CAPpotiFTI$CCA[[i]][,2]<-CAPpotiFTI,"
>
> for(i in c(2:8,15)) CAPpotiFTI$CCA[[i]][,1]<-CAPpotiFTI$CCA[[i]][,1]*-1
> Erro em CAPpotiFTI$CCA[[i]] : índice fora de limites (index out of limits)
>
> Well, it needs lots of patience...
>
> --------------------------------------------------
> From: "Mark Difford" <mark_difford at yahoo.co.uk>
> Sent: Tuesday, October 07, 2008 3:50 PM
> To: <r-help at r-project.org>
> Subject: Re: [R] Mirror Image on Biplot Graphic
>
>>
>> Hi Rodrigo,
>>
>> Again an error, as that doesn't touch one of the data structures. You
>> need
>> to extend the range to include #15, as below:
>>
>> ## This does axis 2
>> mynew.cca <- my.cca
>> for (i in c(2:8,15)) mynew.cca$CCA[[i]][, 2] <- mynew,cca$CCA[[i]][, 2]
>> * -1
>>
>> Cheers, Mark.
>>
>>
>> Mark Difford wrote:
>>>
>>> Hi Rodrigo,
>>>
>>> I looked through my scripts and found my old hack. __WARNING__: Be very
>>> careful to check that
>>> the mirror isn't broken and that all is in order! Make sure that you are
>>> reversing the axes you want. In your original post you mention axis 2,
>>> i.e. y-axis. Below you have used axis 1.
>>>
>>> ## This does axis 2
>>> mynew.cca <- my.cca
>>> for (i in 2:8) mynew.cca$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.
>>>>
>>>> --------------------------------------------------
>
>>>> 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.
>>>>
>>>>
>>>
>>>
>>
>> --
>> View this message in context:
>> http://www.nabble.com/Mirror-Image-on-Biplot-Graphic-tp19857549p19864798.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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