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