On Fri, 16 Jan 2009, r-help-requ...@r-project.org wrote:
Date: Thu, 15 Jan 2009 13:29:03 +0100
From: Pablo G Goicoechea <pgoikoet...@neiker.net>
Subject: Re: [R] How to create a chromosome location map by locus ID
To: Sake <tlep.nav.e...@hccnet.nl>
Cc: r-help@r-project.org
Message-ID: <496f2c0f.3040...@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: dav...@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
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