Thanks Tengfei, That would be fantastic. In the past I have been writing genome browsers with bioperl and ensembl code so gviz was more natural to me, but as a convinced ggplot user I want to add ggbio also to my toolkit, it seems a very nice package, and do many of the things that I have implemented myself with core graphics but nicer. On Mon, Jul 15, 2013 at 5:48 PM, Tengfei Yin <yintengfei@gmail.com> wrote: > Hi Pablo, > > Thanks for your feedback and sorry for the late fix, I have been busy with > something else recently, but I promise I will fix ggbio in devel branch > this week, and update with the new developed features. > > Tengfei > > > On Mon, Jul 15, 2013 at 12:59 AM, Pablo marin-garcia < > harpactocrates@gmail.com> wrote: > >> Thanks Micheal, >> >> Someone know if ggbio would be fixed in devel shortly?. >> >> ggbio is not part of my toolkit yet (I wanted to add it to complement >> gviz, but as I need to use the 2.13 bioc, seems I will wait a bit longer >> ;-). I would skip genomic plotting from the packages I use or run gviz >> instead when in devel) >> >> I know that working in devel is walking the cutting edge but I need the >> features of some packages that are only in devel and I still don't have the >> bioconductor-R-oo knowledge/skills to backport its updates to stable >> versions. >> >> Thanks >> >> Pablo >> >> >> On Thu, Jul 11, 2013 at 2:17 PM, Michael Lawrence < >> lawrence.michael@gene.com> wrote: >> >>> keepSeqlevels and friends have been converted to ordinary functions >>> (rather than generics with methods); Martin fixed that for ggbio, but it >>> looks like ggbio is currently totally broken in devel, and the new version >>> is not propagating. >>> >>> Michael >>> >>> >>> On Wed, Jul 10, 2013 at 5:41 PM, Pablo marin-garcia < >>> harpactocrates@gmail.com> wrote: >>> >>>> Hello, >>>> >>>> I am using R3.0 bioconductor 2.13, ggbio 1.9.2 and GenomicRanges >>>> 1.13..26 >>>> >>>> and when loading ggbio I have the following warning/error: >>>> >>>> || Loading required package: ggbio >>>> || No methods found in "GenomicRanges" for requests: >>>> keepSeqlevels, >>>> renameSeqlevels >>>> || Need specific help about ggbio? try mailing >>>> || the maintainer or visit http://tengfei.github.com/ggbio/ >>>> || >>>> || Attaching package: ^Xggbio^Y >>>> >>>> >>>> I have been following the GenomicRanges thread about keepseqlevel >>>> deprecation and in >>>> >>>> http://permalink.gmane.org/gmane.science.biology.informatics.cond uctor.devel/4378 >>>> Valerie >>>> Obenchain said that from GR 1.13.16 it has been restored but as a >>>> seqleveles() wrappers not generics with methods. >>>> >>>> Q: So, seems to me that ggbio still is trying to access the old >>>> keepseqleveles. Is this error preventing ggbio to work properly in some >>>> circumstances? >>>> >>>> Related with that. I am an experienced programmer but my knowledge of >>>> bioconductor and S4 objects in R is still limited. I have some copy >>>> paste >>>> code that was using keepseqlevels, I can redo many of the code following >>>> the ?seqlevels examples, but I tried > ?keepseqlevels and >keepseqlevels >>>> but nothing was returned. >>>> >>>> Q: How can I see if keepseqlevels is still in GenomicRanges and how it >>>> is >>>> implemented and how to use it (instead of using my own wrappers to >>>> seqlevels;-))? >>>> >>>> Thanks >>>> >>>> Pablo >>>> >>>> [[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]]