Hi All Revisiting this thread to see if there is any update with regards to status of visnab. I guess every now and then I try to look for an interactive plotting solution in R. Any update on the current status would be helpful I guess. Thanks! -Abhi On Mon, Jan 7, 2013 at 10:25 AM, Abhishek Pratap <apratap@lbl.gov> wrote: > Thanks all. > > @Tim : had no idea about Scribl but from the initial glace looks pretty > neat > > -A > > On Fri, Jan 4, 2013 at 4:37 PM, Tim Triche, Jr. <tim.triche@gmail.com>wrote: > >> A shiny version of visnab would be insanely great. Might be possible to >> farm out at least some of the heavy lifting for eg Circos style plots to >> d3, which is also insanely great. >> >> Off topic, but have you played with Scribl at all? It seemed fairly >> usable for some of the tasks I find IGV handles. >> >> I can't say I will miss IGV if something better (webbier) comes along, >> but it is extensible in some important respects. The extending does take >> some work, though, and Java would not be my first choice for writing >> extensions if R and/or JS alternatives are available. >> >> --t >> >> On Jan 4, 2013, at 3:58 PM, Michael Lawrence <lawrence.michael@gene.com> >> wrote: >> >> > The visnab package has different goals from IGV. It aims to provide an >> extensible, R-based platform for interactive genomic visualization. >> Currently, IGV isn't very extensible at all, i.e., no plugin support, some >> nice scripting capabilities via its HTTP interface but no callback >> handling. We decided to focus our energy on ggbio for a while, but Tengfei >> is still very much interested in pushing visnab forward. It is currently >> implemented on top of the R/Qt interface. One idea that has been floated is >> a port to the web browser, while retaining R callback support, via >> something like shiny. Over the holidays, I started porting the qtpaint API >> to javascript and the HTML5 canvas. So the foundations are forming. >> > >> > Michael >> > >> > >> > >> > On Fri, Jan 4, 2013 at 3:17 PM, Tim Triche, Jr. <tim.triche@gmail.com> >> wrote: >> >> IGV would seem to have obsoleted some aspects of visnab. >> >> >> >> ggbio, on the other hand, is awesome, as is Gviz. Perhaps those may >> meet >> >> your needs? Tengfei has certainly been pouring effort into ggbio, and >> Gviz >> >> is also released. the two are complementary IMHO >> >> >> >> >> >> >> >> >> >> On Fri, Jan 4, 2013 at 2:41 PM, Dan Tenenbaum <dtenenba@fhcrc.org> >> wrote: >> >> >> >> > Hi Abhishek, >> >> > >> >> > On Fri, Jan 4, 2013 at 2:32 PM, Abhishek Pratap <apratap@lbl.gov> >> wrote: >> >> > > I saw an old note to myself that I wrote a while ago to check on >> >> > > visnab...and I dont see it as part of bioC as of now. Can anyone >> who is >> >> > > aware of the developments give me an update on the status of the >> >> > package. I >> >> > > am interested in playing with it. >> >> > >> >> > According to this github page: >> >> > >> >> > https://github.com/tengfei/visnab/wiki/Installation- Instruction >> >> > >> >> > visnab is not released to BioC yet. >> >> > >> >> > Perhaps Tengfei can give us a further status update. >> >> > >> >> > Dan >> >> > >> >> > >> >> > >> >> > >> >> > > >> >> > > Thanks! >> >> > > -Abhi >> >> > > >> >> > > [[alternative HTML version deleted]] >> >> > > >> >> > > _______________________________________________ >> >> > > Bioconductor mailing list >> >> > > Bioconductor@r-project.org >> >> > > https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> > > Search the archives: >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > >> >> > _______________________________________________ >> >> > Bioconductor mailing list >> >> > Bioconductor@r-project.org >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> > Search the archives: >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > >> >> >> >> >> >> >> >> -- >> >> *A model is a lie that helps you see the truth.* >> >> * >> >> * >> >> Howard Skipper< >> http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf> >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor@r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]

Hi Abhi, Thanks for your attention, if you are interested in trying visab, I fixed some bugs couple days ago in github, you can try to play with it, but it only provides a minimal bam file viewer/some infrastructures for now, examples command is here https://github.com/tengfei/visnab/blob/master/inst/example/coveragevie w.R Just change the file to your own bam file, those commands will give you a GUI and for coverage view for bam files, it estimates coverage very fast for your genome, so use the search bar to search chromosome names like 'chr1', 'chr3' or gene symbols(pass to widget function your annotation GRanges), or you can use key board(crtl +/-/0) and mouse to zoom in/out and it shows different details at different levels. Just note that it's very rough and for demo purpose only, some GUI functionality won't work such as brush mode, but as always, any feedback are welcome, you can report issues in github. Next step(if I have more free time later) would be supporting TranscriptDb object and finish tracks function, so at least make it available for aligning features. Thanks Tengfei On Thu, May 9, 2013 at 12:45 PM, Abhishek Pratap <apratap@lbl.gov> wrote: > Hi All > > Revisiting this thread to see if there is any update with regards to status > of visnab. I guess every now and then I try to look for an interactive > plotting solution in R. > > Any update on the current status would be helpful I guess. > > > Thanks! > -Abhi > > > On Mon, Jan 7, 2013 at 10:25 AM, Abhishek Pratap <apratap@lbl.gov> wrote: > > > Thanks all. > > > > @Tim : had no idea about Scribl but from the initial glace looks pretty > > neat > > > > -A > > > > On Fri, Jan 4, 2013 at 4:37 PM, Tim Triche, Jr. <tim.triche@gmail.com> >wrote: > > > >> A shiny version of visnab would be insanely great. Might be possible to > >> farm out at least some of the heavy lifting for eg Circos style plots to > >> d3, which is also insanely great. > >> > >> Off topic, but have you played with Scribl at all? It seemed fairly > >> usable for some of the tasks I find IGV handles. > >> > >> I can't say I will miss IGV if something better (webbier) comes along, > >> but it is extensible in some important respects. The extending does take > >> some work, though, and Java would not be my first choice for writing > >> extensions if R and/or JS alternatives are available. > >> > >> --t > >> > >> On Jan 4, 2013, at 3:58 PM, Michael Lawrence <lawrence.michael@gene.com> > > >> wrote: > >> > >> > The visnab package has different goals from IGV. It aims to provide an > >> extensible, R-based platform for interactive genomic visualization. > >> Currently, IGV isn't very extensible at all, i.e., no plugin support, > some > >> nice scripting capabilities via its HTTP interface but no callback > >> handling. We decided to focus our energy on ggbio for a while, but > Tengfei > >> is still very much interested in pushing visnab forward. It is currently > >> implemented on top of the R/Qt interface. One idea that has been > floated is > >> a port to the web browser, while retaining R callback support, via > >> something like shiny. Over the holidays, I started porting the qtpaint > API > >> to javascript and the HTML5 canvas. So the foundations are forming. > >> > > >> > Michael > >> > > >> > > >> > > >> > On Fri, Jan 4, 2013 at 3:17 PM, Tim Triche, Jr. <tim.triche@gmail.com> > > >> wrote: > >> >> IGV would seem to have obsoleted some aspects of visnab. > >> >> > >> >> ggbio, on the other hand, is awesome, as is Gviz. Perhaps those may > >> meet > >> >> your needs? Tengfei has certainly been pouring effort into ggbio, > and > >> Gviz > >> >> is also released. the two are complementary IMHO > >> >> > >> >> > >> >> > >> >> > >> >> On Fri, Jan 4, 2013 at 2:41 PM, Dan Tenenbaum <dtenenba@fhcrc.org> > >> wrote: > >> >> > >> >> > Hi Abhishek, > >> >> > > >> >> > On Fri, Jan 4, 2013 at 2:32 PM, Abhishek Pratap <apratap@lbl.gov> > >> wrote: > >> >> > > I saw an old note to myself that I wrote a while ago to check on > >> >> > > visnab...and I dont see it as part of bioC as of now. Can anyone > >> who is > >> >> > > aware of the developments give me an update on the status of the > >> >> > package. I > >> >> > > am interested in playing with it. > >> >> > > >> >> > According to this github page: > >> >> > > >> >> > https://github.com/tengfei/visnab/wiki/Installation- Instruction > >> >> > > >> >> > visnab is not released to BioC yet. > >> >> > > >> >> > Perhaps Tengfei can give us a further status update. > >> >> > > >> >> > Dan > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > > > >> >> > > Thanks! > >> >> > > -Abhi > >> >> > > > >> >> > > [[alternative HTML version deleted]] > >> >> > > > >> >> > > _______________________________________________ > >> >> > > Bioconductor mailing list > >> >> > > Bioconductor@r-project.org > >> >> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >> > > Search the archives: > >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> >> > > >> >> > _______________________________________________ > >> >> > Bioconductor mailing list > >> >> > Bioconductor@r-project.org > >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >> > Search the archives: > >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> >> > > >> >> > >> >> > >> >> > >> >> -- > >> >> *A model is a lie that helps you see the truth.* > >> >> * > >> >> * > >> >> Howard Skipper< > >> http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf> > >> >> > >> >> [[alternative HTML version deleted]] > >> >> > >> >> _______________________________________________ > >> >> Bioconductor mailing list > >> >> Bioconductor@r-project.org > >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 [[alternative HTML version deleted]]