[BioC] Gene list ideogram

Daniel Brewer daniel.brewer at icr.ac.uk
Thu Nov 5 16:57:55 CET 2009


In the end I used the prepareGenomePlot() function from the quantsmooth 
library followed by text()

library(quantsmooth)
pdf("Indogram.pdf")
peevy <- prepareGenomePlot(data.frame(CHR=locTable$CHR, 
MapInfo=abs(locTable$Loc)), paintCytobands=T, organism="hsa", 
sexChromosomes=T)
text(peevy[,2],peevy[,1]+0.1,locTable$Symbol,adj=c(0,0.5),srt=90,cex=0.5)
dev.off()

The only issue I am having is that sometimes the genes names overlap and 
so I have to manual separate them using inkscape.

Dan

On 05/11/2009 2:24 PM, Vincent Carey wrote:
> over what scale?  geneplotter's cPlot function may be relevant
>
> On Thu, Nov 5, 2009 at 4:27 AM, Daniel Brewer<daniel.brewer at icr.ac.uk>  wrote:
>> Hello,
>>
>> I have a gene list with each genes location and I would like to plot an
>> ideogram with shows where each of these genes are located.  What is the best
>> way to do this?  Its for a paper so I need it to be of high quality.
>>
>> Thanks
>>
>> Dan
>>
>> --
>> **************************************************************
>> Daniel Brewer, Ph.D.
>>
>> Institute of Cancer Research
>> Molecular Carcinogenesis
>> Email: daniel.brewer at icr.ac.uk
>> **************************************************************
>>
>> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
>> Company Limited by Guarantee, Registered in England under Company No. 534147
>> with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
>>
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-- 
**************************************************************

Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
MUCRC
15 Cotswold Road
Sutton, Surrey SM2 5NG
United Kingdom

Tel: +44 (0) 20 8722 4109

**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the a...{{dropped:2}}



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