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
