R help - Sep 2009 - "biplot" graphical options?

Dear R-help fellows

good afternoon.

I am struggling in the attempt to impose some graphical conditions (changing
point symbols, colors, etc) to biplot function (I am using it to visualize the
results of princomp) but I can't apparently manage to change anything but
the axis... and I have been browsing manuals and vignettes without finding any
explicit suggestions on how to operate...

Can anyone, please, point my attention to the relevant documentation?

Thank you in advance and best regards,
Marco

-- 
Marco Manca, MD
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)
PO Box 616
6200 MD Maastricht

E-mail: m.manca at path.unimaas.nl
Office telephone: +31(0)433874633
Personal mobile: +31(0)626441205
Twitter: @markomanka


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Taking the example from ?biplot.princomp with reproducible code (hint,
hint):

biplot(princomp(USArrests))
biplot(princomp(USArrests), col=c(2,3), cex=c(1/2, 2)) 

clearly changes the color and font size on my system. For changing the
"point symbols" (which are text by default), try setting xlabs and
ylabs. But of course, an argument "pch" will not have any effect, as
biplot does have no call to "points" or similar, but to
"text" only (and
hence mainly parameters of "text" will have an effect on what you aim
at). So for documentation, I'd propose ?biplot.princomp and
?biplot.default.

For changes that are truly impossible (there are indeed some), take the
code for biplot.default (or biplot.princomp) and amend where necessary
to fulfill your needs. 

HTH, Michael
> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Manca Marco (PATH)
> Sent: Mittwoch, 2. September 2009 13:02
> To: r-help at r-project.org
> Subject: [R] "biplot" graphical options?
> Importance: High
> 
> 
> Dear R-help fellows
> 
> good afternoon.
> 
> I am struggling in the attempt to impose some graphical 
> conditions (changing point symbols, colors, etc) to biplot 
> function (I am using it to visualize the results of princomp) 
> but I can't apparently manage to change anything but the 
> axis... and I have been browsing manuals and vignettes 
> without finding any explicit suggestions on how to operate...
> 
> Can anyone, please, point my attention to the relevant documentation?
> 
> Thank you in advance and best regards,
> Marco
> 
> --
> Marco Manca, MD
> University of Maastricht
> Faculty of Health, Medicine and Life Sciences (FHML) 
> Cardiovascular Research Institute (CARIM) PO Box 616 6200 MD 
> Maastricht
> 
> E-mail: m.manca at path.unimaas.nl
> Office telephone: +31(0)433874633
> Personal mobile: +31(0)626441205
> Twitter: @markomanka
> 
> 
> **************************************************************
> *******************************************************
> 
> This email and any files transmitted with it are 
> confide...{{dropped:15}}
> 
> ______________________________________________
> R-help at 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.
>

Hi
I had similar problem some time ago. I was advised to use eqscplot  but it 
did not suite my purpose so I used a little twist of biplot. (I added a 
result)


fit<-princomp(some.data, cor=T)

biplot(fit, xlabs=rep("", no.of.poins)) #biplot without points

#some scaling of plot parameters

rrr<-apply(fit$scores[,1:2],2, range)
(abs(rrr)+.1)*sign(rrr)
par(usr=as.vector(rrr))

# plot the points according to some leves
points(fit$scores[,1:2], 
col=jet.colors(11)[(as.numeric(kvalita.ag$typ[cc]))], pch=20)

So my advice is to plot without points and then add points from fit and 
treat them in usual way (pch, col, cex, ...)

Or you could modify source code for biplot and create your own, which 
could by quite tricky.

Regards
Petr




r-help-bounces at r-project.org napsal dne 02.09.2009 13:02:27:
> 
> Dear R-help fellows
> 
> good afternoon.
> 
> I am struggling in the attempt to impose some graphical conditions 
(changing 
> point symbols, colors, etc) to biplot function (I am using it to 
visualize the
> results of princomp) but I can't apparently manage to change anything 
but the 
> axis... and I have been browsing manuals and vignettes without finding 
any 
> explicit suggestions on how to operate...
> 
> Can anyone, please, point my attention to the relevant documentation?
> 
> Thank you in advance and best regards,
> Marco
> 
> -- 
> Marco Manca, MD
> University of Maastricht
> Faculty of Health, Medicine and Life Sciences (FHML)
> Cardiovascular Research Institute (CARIM)
> PO Box 616
> 6200 MD Maastricht
> 
> E-mail: m.manca at path.unimaas.nl
> Office telephone: +31(0)433874633
> Personal mobile: +31(0)626441205
> Twitter: @markomanka
> 
> 
> 
*********************************************************************************************************************
> 
> This email and any files transmitted with it are 
confide...{{dropped:15}}
> 
> ______________________________________________
> R-help at 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.

Hi, You can make a biplot on Your own, it is not so hard. And in this
case You can change parameters for every low level function as You
wish.

PC <- prcomp (iris[,1:4])
lambda <- PC$sdev * sqrt(nrow(PC$x))
plot (t(t(PC$x)/lambda),pch=16,col=as.numeric(iris[,5]))
par (new=T)
Rot <- t(t(PC$rotation)*lambda)
XLIM <- c(-max(abs(Rot[,1])),max(abs(Rot[,1])))
XLIM <- XLIM+(XLIM*0.1)
plot(Rot,col=4,axes=FALSE,xlim=XLIM,ylim=XLIM,pch="")
arrows (rep(0,nrow(PC$rotation)),rep(0,nrow(PC$rotation)),Rot[,1],Rot[,2],col=4)
text (Rot[,1:2],rownames(Rot),col=6)
axis (3)
axis (4)

Best regards,
Andris

On Wed, Sep 2, 2009 at 1:02 PM, Manca Marco
(PATH)<m.manca at path.unimaas.nl> wrote:
>
> Dear R-help fellows
>
> good afternoon.
>
> I am struggling in the attempt to impose some graphical conditions
(changing point symbols, colors, etc) to biplot function (I am using it to
visualize the results of princomp) but I can't apparently manage to change
anything but the axis... and I have been browsing manuals and vignettes without
finding any explicit suggestions on how to operate...
>
> Can anyone, please, point my attention to the relevant documentation?
>
> Thank you in advance and best regards,
> Marco
>
> --
> Marco Manca, MD
> University of Maastricht
> Faculty of Health, Medicine and Life Sciences (FHML)
> Cardiovascular Research Institute (CARIM)
> PO Box 616
> 6200 MD Maastricht
>
> E-mail: m.manca at path.unimaas.nl
> Office telephone: +31(0)433874633
> Personal mobile: +31(0)626441205
> Twitter: @markomanka
>
>
>
*********************************************************************************************************************
>
> This email and any files transmitted with it are confide...{{dropped:15}}
>
> ______________________________________________
> R-help at 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.
>

Manca Marco (PATH <m.manca <at> path.unimaas.nl> writes:
. 
> I am struggling in the attempt to impose some graphical conditions
(changing
point symbols, colors, etc)
> to biplot function (I am using it to visualize the results of princomp) but
I
can't apparently manage to
> change anything but the axis... and I have been browsing manuals and
vignettes
without finding any
> explicit suggestions on how to operate...
> 
> Can anyone, please, point my attention to the relevant documentation?
Howdy,

The relevant documentation in this case is ?biplot. The documentation to the
specific method is less useful (?biplot.princomp). That documentation tells you
that you can't do what you want to do. No choice. For instance, col (for
colour)
can be of length 2 giving different colours for each set of points, but you
cannot vary the colour within the set. Further, you cannot turn off using arrows
and text or even suppress the plotting and add your own points. 

If you use RSiteSearch("biplot"), you can find some packages with more
flexibility than stats:::biplot.princomp and stats:::biplot.default. Another
alternative is to write your own biplot function or do the plot by hand using
the basic commands.

Best wishes, Jari Oksanen