[BioC] chromosome ordering in cPlot()/cColor()

[Axel.Klenk at Actelion.Com]

Dear Biocore Team,

I'm using cPlot()/cColor() from package annotate to produce chromosome
plots and
am very impressed how easily this can be achieved. However, unfortunately,
the
chromosomes are plotted in reverse alphabetical order, i.e. 1, 10, 11, etc.
from bottom
to top and I would like to reorder them to 1, 2, 3, ... from top to bottom
but cannot find an
easy way to do so... am I missing something here?

I managed to get what I want by hacking buildChromLocation() but that's
ugly and I don't
want to maintain a modified function if not necessary.

Would it be possible to add a replace method for the chromInfo slot to
allow e.g.

z <- buildChromLocation("hgug41112a")
library("gtools") # for mixedsort()
info <- chromInfo(z)
chromInfo(z) <- info[rev(mixedsort(names(info)))]

or maybe you can think of a better solution?

Thanks in advance,

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
Switzerland



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