[BioC] cPlot

[Martin Morgan]

Lavinia Gordon wrote:
>    Dear All,
>    Following on from Axels email, this is exactly what I would like to do, but
>    I am not using Affymetrix data.  Can anyone give me some pointers on how to
>    create  an  Bioconductor  data package (i.e. like hgug41112a), but for
>    NimbleGen data.

Hi Lavinia -- you can create your own annotation packages following
instructions in the 'SqlForge' vignette associated with the
AnnotationDbi package, available here, for instance

http://bioconductor.org/packages/2.4/bioc/html/AnnotationDbi.html

If that is not appropriate (e.g., non-model organism) then for this
particular case (using cPlot) you could try to construct a
'chromLocation' object from information you've obtained from other
sources (e.g., NimbleGen) about chromosome location of each probe. There
are hints on what this should look like on the help page
?"chromLocation-class"; you're aiming to be able to call 'new' with
appropriate arguments. Some other hints about what the data is supposed
to look like might come from inspecting the object 'z' produced by the
code in the cPlot example.

Martin



>    with many thanks for your time,
>    Lavinia Gordon.
> 
>      Message: 6
>      Date: Mon, 24 Aug 2009 19:15:29 +0200
>      From: Axel.Klenk at Actelion.Com
>      Subject: [BioC] chromosome ordering in cPlot()/cColor()
>      To: bioconductor at stat.math.ethz.ch
>      Message-ID:
>              <12450_1251134133_4A92CAB5_12450_361234_1_OFDD2C6357.89EE7981-ONC1
>      25761C.005CC5F4-C125761C.005ECE81 at actelion.com>
> 
>      Content-Type: text/plain; charset=US-ASCII
>      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
> 
>    Lavinia Gordon
>    Research Officer
>    Bioinformatics
>    Murdoch Childrens Research Institute
>    Royal Children's Hospital
>    Flemington Road Parkville Victoria 3052 Australia
>    telephone: +61 3 8341 6221
>    [1]www.mcri.edu.au
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