I need to make a graphic to show problems on different parts of chromosomes (think of a graphic showing the number of frayed threads as colors along different parts of a worn out rope). I want to draw bars going from left to right across a page and color different parts of the bars in different shades. Each graphic will need to have several bars of different lenghts corresponding to the different lenghts of the chromsomes. Is there a package around that can help me draw custom bars of different colors? I am a hardcore SAS guy who is just learning R so I am mostly clueless.
arrows and I don't remember what package, but I will see if I can remember. On Tue, Dec 9, 2008 at 3:02 PM, Raymond Balise <iteachtyping at gmail.com> wrote:> I need to make a graphic to show problems on different parts of > chromosomes (think of a graphic showing the number of frayed threads > as colors along different parts of a worn out rope). I want to draw > bars going from left to right across a page and color different parts > of the bars in different shades. Each graphic will need to have > several bars of different lenghts corresponding to the different > lenghts of the chromsomes. > > Is there a package around that can help me draw custom bars of > different colors? I am a hardcore SAS guy who is just learning R so I > am mostly clueless. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis
Hi Raymond, You might be able to get the plots you want with the 'cytoband' material provided in the Bioconductor package "SNPchip". Check out the SNPchip data set 'cytoband' and the plot function "plotCytoband" for ideas. This material is used e.g. in Bioconductor package "VanillaICE" to add a chromosome graphic to the bottom of data plots of genomic data. You can see examples in the vignette PDFs. HTH Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney at bccrc.ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada> -----Original Message----- > From: r-help-bounces at r-project.org[mailto:r-help-bounces at r-project.org]> On Behalf Of stephen sefick > Sent: Tuesday, December 09, 2008 7:48 PM > To: Raymond Balise > Cc: r-help at r-project.org > Subject: Re: [R] How can I draw bars > > arrows and I don't remember what package, but I will see if I can > remember. > > On Tue, Dec 9, 2008 at 3:02 PM, Raymond Balise<iteachtyping at gmail.com>> wrote: > > I need to make a graphic to show problems on different parts of > > chromosomes (think of a graphic showing the number of frayed threads > > as colors along different parts of a worn out rope). I want to draw > > bars going from left to right across a page and color differentparts> > of the bars in different shades. Each graphic will need to have > > several bars of different lenghts corresponding to the different > > lenghts of the chromsomes. > > > > Is there a package around that can help me draw custom bars of > > different colors? I am a hardcore SAS guy who is just learning R soI> > am mostly clueless. > > > > ______________________________________________ > > R-help at r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > > > > -- > Stephen Sefick > > Let's not spend our time and resources thinking about things that are > so little or so large that all they really do for us is puff us up and > make us feel like gods. We are mammals, and have not exhausted the > annoying little problems of being mammals. > > -K.Mullis> > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code.
Raymond Balise wrote:> I need to make a graphic to show problems on different parts of > chromosomes (think of a graphic showing the number of frayed threads > as colors along different parts of a worn out rope). I want to draw > bars going from left to right across a page and color different parts > of the bars in different shades. Each graphic will need to have > several bars of different lenghts corresponding to the different > lenghts of the chromsomes. > > Is there a package around that can help me draw custom bars of > different colors? I am a hardcore SAS guy who is just learning R so I > am mostly clueless. >Hi Raymond, The gradient.rect and color.scale functions (in plotrix) may not do exactly what you want, but the code within them is almost certainly relevant to your problem. Jim