[R] R-help Digest, Vol 71, Issue 16

[David Duffy]

On Fri, 16 Jan 2009, r-help-request at r-project.org wrote:
> Date: Thu, 15 Jan 2009 13:29:03 +0100
> From: Pablo G Goicoechea <pgoikoetxea at neiker.net>
> Subject: Re: [R] How to create a chromosome location map by locus ID
> To: Sake <tlep.nav.ekas at hccnet.nl>
> Cc: r-help at r-project.org
> Message-ID: <496F2C0F.3040304 at neiker.net>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Sake:
> If you do not find an answer within the list, MapChart will probably do
> what you want (without the fancy chromosomal bands, though). You can
> find it at
>
> http://www.biometris.wur.nl/uk/Software/MapChart/
>
> Hope this helps
>
> Sake escribi?:
>> Hi,
>>
>> I'm trying to make a chromosomal map in R by using the locus. I have a list
>> of genes and their locus, and I want to visualise that so you can see if
>> there are multiple genes on a specific place on a chromosome. A example of
>> what I more or less want is below:
>> http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG
>> The genes and locus are here:
>> http://www.nabble.com/file/p21474206/genlocus.csv genlocus.csv
>> I've tried some things, but nothing worked like I would like it to see.
>> Maybe there is some kind of package that does this for you, but I did not
>> find it yet.
>> Thanx
>>
>> Sake
>>

You could probably use the functions in my lodplot package (it includes the
chromosomal band coordinates used by the NCBI Mapviewer)

?chrom.bands
?paint.chromosome

Maybe something like (will need tinkering):

plot(cbind(locus_coordinate[chrom==1],
            rep(2, length(locus_coordinate)[chrom==1]),
      axes=F, xlab=" ", ylab=" "))
paint.chromosome(1, pos=2.2)
points(cbind(locus_coordinate[chrom==1],
              rep(2, length(locus_coordinate)[chrom==1]),
        col="red", cex=4)

Unfortunately for you, the units here are cM ;).

David Duffy.

-- 
| David Duffy (MBBS PhD)                                         ,-_|\
| email: davidD at qimr.edu.au  ph: INT+61+7+3362-0217 fax: -0101  /     *
| Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
| 300 Herston Rd, Brisbane, Queensland 4029, Australia  GPG 4D0B994A v