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
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