[BioC] magnifying genenames in pamr.plotcen()

[James W. MacDonald]

Hi Benjamin,


Benjamin Otto wrote:
> Hi,
> 
> plotting the centroids of three parameters with pamr.plotcen() results in
> tiny "genenames" that can hardly be read and a really weird space
> consumption in the plot. It looks about that:
> 
> +------------------------------+
> |                              |
> |                              |
> |                              |
> |        J          N          |
> |                              |
> |                              |
> |                              |
> |                              |
> |   xxx +-----     ---+        |
> |       |             |        |
> |   xxx +---        --+        |
> |       |             |        |
> |   xxx +--          -+        |
> +------------------------------+
> 
> There would be enough space for the lower part of the plot (the one
> containing the centroids and genenames) to be stretched vertically much
> more. Then the genenames font could be even bigger and more readable. I had
> a look at the function header of pamr.plotcen() but unfortunately there is
> no corresponding argument. Is there anyway to get the function plot that
> thing in a more reasonable fashion?

The example for pamr.plotcen() doesn't look quite like that, so maybe it 
has something to do with the number of genes that are being plotted in 
your case. Anyway, there isn't a variable for the text size, so you will 
need to modify the code yourself if you want this added functionality 
(or plead your case with the maintainer, Rob Tibshirani).

All you would need to do is add a cex argument (say cex = 0.4), and then 
modify the last line of the function to read

text(rep(0, nd), seq(nd), label = g, cex = cex, adj = 0,
         col = 1)

You can call this function something different like my.pamr.plotcen, 
save it as my.pamr.plotcen.R, and source() it into your R session.

Then call my.pamr.plotcen(<whatever arguments>, cex = 0.7).

HTH,

Jim


> 
> regards
> 
> Benjamin
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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