Thank you, Tengfei. I have the script handy, as I am would like to generate
One Image per Gene Region :
I could email it to you shortly, for the moment when you will have more
time available.  Thanks so much.


On Tue, Oct 8, 2013 at 2:02 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote:

> To me this is a very interesting feature request, it's more like multiple
> gene regions for tracks, you are talking about 200 regions, make it hard to
> fit into one screen, I am thinking about make a function to generate
> animation of many gene regions of different tracks,  with package
> animation, so you could either output the 200 hundred figures into a folder
> or go over the regions with Javascript control button in your internet
> browser.
>
> I don't have a function like that in ggbio to support viewing 200 regions
> of trakcs, but I could probably provide a scripts to you for that purpose.
>
> Tengfei
>
>
> On Tue, Oct 8, 2013 at 4:55 PM, Bogdan Tanasa <tanasa@gmail.com> wrote:
>
>> Thank you all. To add a brief description about my project :
>>
>> I have a long list  of GENE REGIONS (200 regions, each region is of type
>> "chr:start-end") and for each region, I would like to display several
>> genomic tracks (eg ChIP-seq peaks, gene annotations, etc etc).
>>
>> I wrote a short script below, using xlim() function. As these 200 regions
>> are distributed over 24 chromosomes, it looks that I may have to split the
>> data for each of these 24 chromosomes, and run the script for every
>> chromosome. Unless  you have another suggestions ...
>>
>> thank you,
>>
>> bogdan
>>
>>
>> On Tue, Oct 8, 2013 at 1:36 PM, Michael Lawrence <
>> lawrence.michael@gene.com> wrote:
>>
>>> What exactly is the problem? The masking should be harmless; the ggplot2
>>> xlim is masked with a generic that will delegate to it by default.
>>>
>>>
>>> On Tue, Oct 8, 2013 at 1:24 PM, Bogdan Tanasa <tanasa@gmail.com> wrote:
>>>
>>>>  Dear all, and Tengfei,
>>>>
>>>> I am getting the following message when loading the package "ggbio",
>>>> particularly that
>>>> "The following objects are masked from ‘package:ggplot2’:" .
>>>>
>>>> I am especially interested in "xlim" function, to work on a GRange
>>>> object.
>>>> Any advice ?
>>>>
>>>> thank you very much,
>>>>
>>>> --- bogdan
>>>>
>>>> -------------------------------------------------------------------
>>>> " > library("ggbio")
>>>>
>>>> Attaching package: ‘ggbio’
>>>>
>>>> The following objects are masked from ‘package:ggplot2’:
>>>>
>>>> geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
>>>> xlim"
>>>> --------------------------------------------------------------------
>>>>
>>>>         [[alternative HTML version deleted]]
>>>>
>>>>
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>>>>
>>>
>>>
>>
>
>
> --
> Tengfei Yin, PhD
> Seven Bridges Genomics
> sbgenomics.com
> 625 Mt. Auburn St. Suite #208
> Cambridge, MA 02138
> (617) 866-0446
>

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