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