Dear Boris, good morning, and thank you for your message. After thinking a bit more yesterday, I believe that I could adapt the functionality of some R packages that display the synteny regions across multiple species (here please see an example Figure 1 from http://www.g3journal.org/ content/7/6/1775.figures-only),
although I have not found yet a R package that does this display (in my case, instead of distinct species, I will just show distinct chromosomes connected by translocations). If you have any suggestions, please let me know. thanks a lot, -- bogdan On Sat, Jul 28, 2018 at 6:42 AM, Boris Steipe <boris.ste...@utoronto.ca> wrote: > Maybe the Bioconductor package "intansv" can help you. You asked for > linear chromosomes, but such data is commonly plotted in Circos plots as > e.g. with the Bioconductor OmicsCircos package (cf. > https://bioconductor.org/packages/devel/bioc/vignettes/ > OmicCircos/inst/doc/OmicCircos_vignette.pdf) > > However the Bioconductor Project has its own support mailing list, R-Help > is for programming help. > > > B. > > > > > On 2018-07-28, at 02:24, Bogdan Tanasa <tan...@gmail.com> wrote: > > > > Dear all, > > > > we wish you a fruitful and refreshing weekend ! Thought that I may also > > write to ask you for a suggestion, specifically if you could please > advise > > on whether there is any package already built (in R) that could help with > > the following data visualization : > > > > > > we have a set of mutations from many cancer samples > > > > we would like to display the POINT MUTATIONS along the chromosome > > coordinates (on the linear scale, ie. HORIZONTALLY) > > > > we would like to display the TRANSLOCATIONS (and GENE FUSIONS), as > > VERTICAL LINES connecting the breakpoints that are located on the > > chromosomes that are represented HORIZONTALLY > > > > Thanks a lot, > > > > -- bogdan > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > 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. > > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.