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.conductor.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]]
>>>>
>>>> _______________________________________________
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>>>> Search the archives:
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>>>>
>>>
>>>
>>
>
>
> --
> Tengfei Yin
> MCDB PhD student
> 1620 Howe Hall, 2274,
> Iowa State University
> Ames, IA,50011-2274
>
>
>

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