[R] Mirror Image on Biplot Graphic
Rodrigo Aluizio
r.aluizio at gmail.com
Tue Oct 7 22:52:59 CEST 2008
Well this time I have to assume, I'm not understanding what is wrong now.
And I have to say: 'Thank You for your patience', cause I'm going crazy
here! :-)
Mark, I tried this:
CAPpotiFTI<-CAPpotiFT
for(i in c(2:8,15)) CAPpotiFTI$CCA[[i]][, 1]<-CAPpotiFTI$CCA[[i]][, 1] * -1
and got this:
Erro em CAPpotiFTI$CCA[[i]] : índice fora de limites (index out of limits)
Here is the script until this point
library(vegan)
library(xlsReadWrite)
#------------------------FT----------------------#
PotiAbioFT<-read.xls('FatorialReplica.xls',sheet=4,rowNames=T)
PotiBioFT<-read.xls('FatorialReplica.xls',sheet=6,rowNames=T)
attach(PotiAbioFT)
LogPotiBioFT<-log(PotiBioFT+1)
CAPpotiFT<-capscale(t(LogPotiBioFT)~Envoronmental+Variables,dist="bray",add=T)
PermCAPFT<-anova.cca(CAPpotiFT,alpha=0.05,model='full',first=F,permutations=999)
PermCAPFT
summary(CAPpotiFT)
# Rotating the axis
CAPpotiFTI<-CAPpotiFT
for(i in c(2:8,15)) CAPpotiFTI$CCA[[i]][, 1]<-CAPpotiFTI$CCA[[i]][, 1] * -1
--------------------------------------------------
From: "Mark Difford" <mark_difford em yahoo.co.uk>
Sent: Tuesday, October 07, 2008 5:17 PM
To: <r-help em r-project.org>
Subject: Re: [R] Mirror Image on Biplot Graphic
>
> Hi Rodrigo,
>
> Yes it does, but this will work. You have erroneously used a "," in your
> call, it should be a ".", if anything. You have also inserted "cca"... And
> the axes being switched must be conformant:
>
>>> CAPpotiFTI<-CAPpotiFT
>>> for(i in c(2:8,15))
>>> CAPpotiFTI$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:
>>
[[elided Yahoo spam]]
>> 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...
>>
>> --------------------------------------------------
>> Sent: Tuesday, October 07, 2008 3:50 PM
>> To: <r-help em 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$biplot),col=323232,cex=0.6,lwd=2,lty='dotted')
>>>>> Doesn't return an error, but it's not a mirror image as expected, it's
>>>>> nonsense.
>>>>>
>>>>> --------------------------------------------------
>>
>>>>> Sent: Tuesday, October 07, 2008 12:22 PM
>>>>> To: <r-help em r-project.org>
>>>>> Subject: Re: [R] Mirror Image on Biplot Graphic
>>>>>
>>>>>>
>>>>>> Hi Rodrigo,
>>>>>>
>>>>>> Sorry again: the structure vegan uses is quite complex. Technically
>>>>>> you
>>>>>> should use the extractor function scores() to extract what you want
>>>>>> from
>>>>>> the
>>>>>> object, e.g. scores(my.cca, display="species") or scores(my.cca,
>>>>>> display="cn") [centroids]. I did work out a quicker way of reversing
>>>>>> axes,
>>>>>> but that seems to have gone walking...and I am not using vegan at the
>>>>>> moment.
>>>>>>
>>>>>> Quickest hack is to make a copy of the objects you want to plot,
>>>>>> reversing
>>>>>> orientations along the way. So do (my.cca is your original object):
>>>>>>
>>>>>> Temp.data <- scores(my.cca, display=c("sites", "species", "cn"))
>>>>>>
>>>>>> ## Reverse yaxes
>>>>>> Temp.data$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.
>>>>>>
>>>>>
>>>>> ______________________________________________
>>>>> 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-tp19857549p19864798.html
>>> Sent from the R help mailing list archive at Nabble.com.
>>>
>>> ______________________________________________
>>> R-help em r-project.org mailing list
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>>> 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-tp19857549p19866348.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help em r-project.org mailing list
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> PLEASE do read the posting guide
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