[R] Mirror Image on Biplot Graphic
Rodrigo Aluizio
r.aluizio at gmail.com
Tue Oct 7 23:49:22 CEST 2008
Exactly. It's solved. Just remove #15.
CAPpotiFTI<-CAPpotiFT
for(i in c(2:8))CAPpotiFTI$CCA[[i]][,1]<-CAPpotiFTI$CCA[[i]][,1]*-1
It seems that I've to pay more attention and study more about R language.
Thanks a lot once more.
Rodrigo.
--------------------------------------------------
From: "Mark Difford" <mark_difford em yahoo.co.uk>
Sent: Tuesday, October 07, 2008 6:34 PM
To: <r-help em r-project.org>
Subject: Re: [R] Mirror Image on Biplot Graphic
>
> Hi Rodrigo,
>
> This is because [I now see] you are working on a capscale object, not a
> cca
> object, which is what I thought you were using. It still works, though,
> even
> with c(2:8,15), though DF #15 doesn't exist in capscale objects. To show
> you
> that this is so, run the example below, which uses a data set from vegan.
> I
> have dropped #15 from the selection set.
>
> ## Ex. of switching axes of capscale object
> windows(); par(mfrow=c(2,2))
> data(varespec)
> data(varechem)
> vare.cap <- capscale(varespec ~ N + P + K + Condition(Al), varechem,
> dist="bray")
> plot(vare.cap)
> for(i in c(2:8)) vare.cap$CCA[[i]][, 1]<-vare.cap$CCA[[i]][, 1] * -1
> plot(vare.cap)
> for(i in c(2:8)) vare.cap$CCA[[i]][, 2]<-vare.cap$CCA[[i]][, 2] * -1
> plot(vare.cap)
> for(i in c(2:8)) vare.cap$CCA[[i]][, 1:2]<-vare.cap$CCA[[i]][, 1:2] * -1
> plot(vare.cap)
>
> Cheers, Mark.
>
>
> Rodrigo Aluizio wrote:
>>
>> 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$CCA[[i]][, 1] *
>> -1
>>
>>
>>
>> --------------------------------------------------
>> Sent: Tuesday, October 07, 2008 5:17 PM
>> To: <r-help em r-project.org>
>> Subject: Re: [R] Mirror Image on Biplot Graphic
>>
>>>
>>> Hi Rodrigo,
>>>
>>> Yes it does, but this will work. You have erroneously used a "," in your
>>> call, it should be a ".", if anything. You have also inserted "cca"...
>>> And
>>> the axes being switched must be conformant:
>>>
>>>>> CAPpotiFTI<-CAPpotiFT
>>>>> for(i in c(2:8,15))
>>>>> CAPpotiFTI$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
>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> PLEASE do read the posting guide
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>>>>>
>>>>
>>>> ______________________________________________
>>>> R-help em r-project.org mailing list
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>>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>>
>>>
>>> --
>>> View this message in context:
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>>> Sent from the R help mailing list archive at Nabble.com.
>>>
>>> ______________________________________________
>>> R-help em r-project.org mailing list
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>>
>> ______________________________________________
>> R-help em r-project.org mailing list
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>> PLEASE do read the posting guide
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>>
>>
>
> --
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> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
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