even better, there is a very good book on how to do graphics in R, called R Graphics, by Paul Murrell, you really should buy it... Sean Davis wrote: > On Wednesday 18 April 2007 10:25, Daniel Brewer wrote: >> Hi, >> >> I am getting really frustrated with trying to create a specific plot. I >> have the following matrix (monkey): >> Exon PRC1 PRC2 PRC3 >> 1 0_110 2.0132845 1.484080 1.923869 >> 2 0_34 2.6528139 1.141114 1.242584 >> 3 0_78 1.6247146 1.230726 1.592407 >> 4 10 1.4471323 1.137777 1.426656 >> 5 11 1.5471201 1.204736 1.500566 >> 6 2 1.0423570 1.104883 1.087180 >> 7 3 0.9563367 1.017354 1.067159 >> 8 4 1.4577586 1.166938 1.422878 >> 9 5 1.5081813 1.177205 1.494983 >> 10 6 1.4432391 1.144851 1.396613 >> 11 7 1.6995243 1.337146 1.643418 >> 12 8 1.3848549 1.096389 1.357165 >> 13 9 1.4995867 1.162944 1.444809 >> >> Exon is the Exon number of a label saying which two exons the probe is >> in-between. That column should be treated as labels, not numeric. >> >> What I would like to be able to do is plot for example PRC1 on the >> y-axis and the Exon as the x-axis labels (just evenly spaced not a >> numeric scale). Secondly I would like to be able to reorder the labels >> for the plot. >> >> The closest I have got is: >> plot(monkey$Exon,monkey$PRC1) > > How about (untested): > > matplot(monkey[,2:4],axes=F) > axis(side=1,labels=as.character(monkey$Exon)) > box() > > Or, if you want only PRC1: > > plot(monkey[,2],axes=F) > > instead of matplot. > > Sean > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

On Wednesday 18 April 2007 10:39, Sean Davis wrote: > On Wednesday 18 April 2007 10:25, Daniel Brewer wrote: > > What I would like to be able to do is plot for example PRC1 on the > > y-axis and the Exon as the x-axis labels (just evenly spaced not a > > numeric scale). Secondly I would like to be able to reorder the labels > > for the plot. I forgot to address your reordering problem. Simply reorder the monkey data frame however you like and the plotting code I just sent should work just fine. (Again, untested....) Sean

Thanks James and Sean, using a combination of the two that worked great. > matplot(monkey[c(6,7,2,8,9,10,11,3,12,13,4,5,1),2:4], xaxt="n") > axis(side=1,at=1:nrow(monkey),labels=as.character(monkey$Exon[c(6,7,2, 8,9,10,11,3,12,13,4,5,1)]),las=2) Excellant. Dan James W. MacDonald wrote: > Hi Dan, > > Daniel Brewer wrote: >> Hi, >> >> I am getting really frustrated with trying to create a specific plot. I >> have the following matrix (monkey): >> Exon PRC1 PRC2 PRC3 >> 1 0_110 2.0132845 1.484080 1.923869 >> 2 0_34 2.6528139 1.141114 1.242584 >> 3 0_78 1.6247146 1.230726 1.592407 >> 4 10 1.4471323 1.137777 1.426656 >> 5 11 1.5471201 1.204736 1.500566 >> 6 2 1.0423570 1.104883 1.087180 >> 7 3 0.9563367 1.017354 1.067159 >> 8 4 1.4577586 1.166938 1.422878 >> 9 5 1.5081813 1.177205 1.494983 >> 10 6 1.4432391 1.144851 1.396613 >> 11 7 1.6995243 1.337146 1.643418 >> 12 8 1.3848549 1.096389 1.357165 >> 13 9 1.4995867 1.162944 1.444809 >> >> Exon is the Exon number of a label saying which two exons the probe is >> in-between. That column should be treated as labels, not numeric. >> >> What I would like to be able to do is plot for example PRC1 on the >> y-axis and the Exon as the x-axis labels (just evenly spaced not a >> numeric scale). Secondly I would like to be able to reorder the labels >> for the plot. >> >> The closest I have got is: >> plot(monkey$Exon,monkey$PRC1) > > Does > > plot(1:dim(monkey)[1], monkey$PRC1, xaxt="n") > axis(1, at=1:dim(monkey)[1], labels = monkey$Exon, las=2) > > do what you want? > > Best, > > Jim > > >> >> But that seems to be producing a boxplot rather than points. If I put >> type="p" it makes no difference and if I try and reorder the matrix it >> does not make any difference either e.g. >> monkey$Exon[c(6,7,2,8,9,10,11,3,12,13,4,5,1)] >> >> monkey$Exon is a factor object >> >> Any help would be great. >> >> Dan >> > > -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research 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 addre...{{dropped}}