Thank you Jeff. Yes, certainly, I posted a message on BioC too, although I have not received any suggestions by now.
On Sat, Jul 28, 2018 at 8:05 AM, Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote: > My suggestion is to pay attention to Boris and ask people who do this kind > of plotting frequently... and they are typically found on the Bioconductor > mailing list, not this list. > > On Sat, 28 Jul 2018, Bogdan Tanasa wrote: > > 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/posti >> ng-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> >> > ------------------------------------------------------------ > --------------- > Jeff Newmiller The ..... ..... Go Live... > DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live > Go... > Live: OO#.. Dead: OO#.. Playing > Research Engineer (Solar/Batteries O.O#. #.O#. with > /Software/Embedded Controllers) .OO#. .OO#. rocks...1k > ------------------------------------------------------------ > --------------- > [[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.
