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

[Martin Morgan]

Martin Morgan <mtmorgan at fhcrc.org> writes:

> Hi Axel --
>
> Axel.Klenk at Actelion.Com writes:
>
>> 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?
>
> As a work-around, you might try
>
>   example(cPlot) # get object z
>   idx <- c("1", "5", "10", "X")
>   zz <- initialize(z, chromLocs=chromLocs(z)[idx], chromInfo(z)[idx])

oops, that should be

  zz <- initialize(z, chromLocs=chromLocs(z)[idx],
                   chromInfo=chromInfo(z)[idx])

>   cPlot(zz)
>   
> I'm not sure whether there are other consequences of this sort of
> change, and if there are it would be good if you would let me know
> before a more permanent solution is implemented.
>
> Martin
>
>> Thanks in advance,
>>
>>  - axel
>>
>>
>> Axel Klenk
>> Research Informatician
>> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
>> Switzerland
>>
>>
>>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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