R help - Jun 2012 - How can I "declutter"/make a biplot less messy in R

I am doing a principle component analysis on a dataset with a lot of
different variables and have constructed a biplot of the data. 
Unfortunately, as can be seen on the attached image, the biplot is very
messy, cluttered, and hard to read.  I have performed a few modifications
including outlier removal from a few of the variables, which has made the
plot better, however it still is too cluttered to read the variable names. 
Is there any further improvment that can be made to the attached plot and if
so what steps should I take?

Thanks,
Derek


http://r.789695.n4.nabble.com/file/n4633703/biplot.jpg 

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Don't do the biplot.  Darn hard to make sense of anyway.  Plot the scores
and the loadings separately.  You can see how to do that in this thread:
http://r.789695.n4.nabble.com/How-to-plot-PCA-output-td4614732.html

Good Luck.  Bryan
***********
Bryan Hanson
Professor of Chemistry & Biochemistry
DePauw University

On Jun 18, 2012, at 10:37 AM, dss wrote:
> I am doing a principle component analysis on a dataset with a lot of
> different variables and have constructed a biplot of the data. 
> Unfortunately, as can be seen on the attached image, the biplot is very
> messy, cluttered, and hard to read.  I have performed a few modifications
> including outlier removal from a few of the variables, which has made the
> plot better, however it still is too cluttered to read the variable names. 
> Is there any further improvment that can be made to the attached plot and
if
> so what steps should I take?
> 
> Thanks,
> Derek
> 
> 
> http://r.789695.n4.nabble.com/file/n4633703/biplot.jpg 
> 
> --
> View this message in context:
http://r.789695.n4.nabble.com/How-can-I-declutter-make-a-biplot-less-messy-in-R-tp4633703.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> ______________________________________________
> 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 Derek,

It's good form to provide an example with code so that we can see what
functions you're using and what you've tried.

I'm going to assume that you're using princomp(). Here's one way to
reduce the clutter:

pc.cr <- princomp(USArrests, cor = TRUE)
biplot(pc.cr, xlabs=rep("x", nrow(USArrests)))

You can also change the colors and the scalings: see
?biplot.princomp
and
?biplot.default
for details.

Outlier removal may not be a good idea.

You also didn't tell us what your intent was: a publication-quality
plot? Something simply for you to look at yourself? Without knowing
that, it's hard to "improve" it.

Sarah

On Mon, Jun 18, 2012 at 10:37 AM, dss <Derek.Schanze at srnl.doe.gov>
wrote:
> I am doing a principle component analysis on a dataset with a lot of
> different variables and have constructed a biplot of the data.
> Unfortunately, as can be seen on the attached image, the biplot is very
> messy, cluttered, and hard to read. ?I have performed a few modifications
> including outlier removal from a few of the variables, which has made the
> plot better, however it still is too cluttered to read the variable names.
> Is there any further improvment that can be made to the attached plot and
if
> so what steps should I take?
>
> Thanks,
> Derek


-- 
Sarah Goslee
http://www.functionaldiversity.org