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$CCA[[i]] : índice fora de limites (index out of limits) > > Well, it needs lots of patience... > > -------------------------------------------------- > From: "Mark Difford" <[EMAIL PROTECTED]> > Sent: Tuesday, October 07, 2008 3:50 PM > To: <r-help@r-project.org> > Subject: Re: [R] Mirror Image on Biplot Graphic > >> >> Hi Rodrigo, >> >> Again an error, as that doesn't touch one of the data structures. You >> need >> to extend the range to include #15, as below: >> >> ## This does axis 2 >> mynew.cca <- my.cca >> for (i in c(2:8,15)) mynew.cca$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@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. >>>> >>>> >>> >>> >> >> -- >> 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@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-tp19857549p19866348.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.