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. >> >> This e-mail message is confidential and for use by the a...{{dropped:2}} >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> -- ************************************************************** 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}}