Re: [R] Mirror Image on Biplot Graphic

Rodrigo Aluizio Tue, 07 Oct 2008 13:55:54 -0700

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 crazyhere! :-)


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" <[EMAIL PROTECTED]>
Sent: Tuesday, October 07, 2008 5:17 PM
To: <r-help@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 existsand

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 oflimits)


Well, it needs lots of patience...

--------------------------------------------------

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 youare

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 makeyour

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 constrainedand

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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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.


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Re: [R] Mirror Image on Biplot Graphic

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