Just put "color" as a column in the RangedData. It can be in any format
accepted by col2rgb().

Michael

On Wed, Aug 5, 2009 at 7:08 AM, rcaloger <raffaele.calogero@gmail.com>wrote:

> Thanks for the info related to the RGB feature I completely missed that
> point when I red the BED format help on the UCSC browser.
> Could please tell me where I can find the instruction to handle the RGB BED
> feature in rtracklayer?
> Cheers
>
> Raffaele
> Michael Lawrence ha scritto:
>
>> On Tue, Aug 4, 2009 at 11:16 AM, rcaloger <raffaele.calogero@gmail.com
>> >wrote:
>>
>>
>>
>>> The BED15 format is quite nice to represent alternative splicing events
>>> data (insertion/skipping), the grey scale of the score from the BED
>>> format
>>> is not ideal. Now, thanks to your implementation of BED15 format I  can
>>> update  the function for visualization of alternative splicing events in
>>> oneChannelGUI package.
>>> Many thanks, again!
>>>
>>>
>>
>>
>> You're welcome. But wouldn't using the item RGB feature of BED get around
>> the grey scale?
>>
>>
>>
>>
>>> Raffaele
>>>
>>> Michael Lawrence ha scritto:
>>>
>>>  I guess we weren't sure if anyone wanted that, so it wasn't implemented.
>>> I
>>>
>>>
>>>> just did though, for version 1.5.10. It's not documented yet, but you
>>>> can
>>>> do
>>>> stuff like:
>>>>
>>>> track(session, format = "bed15", expNames = c("samp1", "samp2")) <-
>>>> myTrack
>>>>
>>>> Where 'myTrack' has columns 'samp1' and 'samp2' containing expression
>>>> values.
>>>>
>>>> Or to output every column, it's just:
>>>>
>>>> track(session, format = "bed15") <- myTrack
>>>>
>>>> If the track was imported from an external Bed15 track, then it's
>>>> automatic:
>>>> track(session) <- myTrack
>>>>
>>>> Hope this works for you,
>>>> Michael
>>>>
>>>> On Mon, Aug 3, 2009 at 8:13 AM, rcaloger <raffaele.calogero@gmail.com
>>>>
>>>>
>>>>> wrote:
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>> Hi,
>>>>> since I am interested to visualize microarray data on the UCSC genome
>>>>> browser I would like to know if  there is the possibility to use the
>>>>> BED15
>>>>>  format for microarray data visualization in rtracklayer.
>>>>> Cheers
>>>>> Raffaele
>>>>>
>>>>> --
>>>>>
>>>>> ----------------------------------------
>>>>> Prof. Raffaele A. Calogero
>>>>> Bioinformatics and Genomics Unit
>>>>> Dipartimento di Scienze Cliniche e Biologiche
>>>>> c/o Az. Ospedaliera S. Luigi
>>>>> Regione Gonzole 10, Orbassano
>>>>> 10043 Torino
>>>>> tel.   ++39 0116705417
>>>>> Lab.   ++39 0116705408
>>>>> Fax    ++39 0119038639
>>>>> Mobile ++39 3333827080
>>>>> email: raffaele.calogero@unito.it
>>>>>    raffaele[dot]calogero[at]gmail[dot]com
>>>>> www:   http://www.bioinformatica.unito.it
>>>>> Info: http://publicationslist.org/raffaele.calogero
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor@stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>> --
>>>
>>> ----------------------------------------
>>> Prof. Raffaele A. Calogero
>>> Bioinformatics and Genomics Unit
>>> Dipartimento di Scienze Cliniche e Biologiche
>>> c/o Az. Ospedaliera S. Luigi
>>> Regione Gonzole 10, Orbassano
>>> 10043 Torino
>>> tel.   ++39 0116705417
>>> Lab.   ++39 0116705408
>>> Fax    ++39 0119038639
>>> Mobile ++39 3333827080
>>> email: raffaele.calogero@unito.it
>>>     raffaele[dot]calogero[at]gmail[dot]com
>>> www:   http://www.bioinformatica.unito.it
>>> Info: http://publicationslist.org/raffaele.calogero
>>>
>>>
>>>
>>>
>>
>>
>>
>
>
> --
>
> ----------------------------------------
> Prof. Raffaele A. Calogero
> Bioinformatics and Genomics Unit
> Dipartimento di Scienze Cliniche e Biologiche
> c/o Az. Ospedaliera S. Luigi
> Regione Gonzole 10, Orbassano
> 10043 Torino
> tel.   ++39 0116705417
> Lab.   ++39 0116705408
> Fax    ++39 0119038639
> Mobile ++39 3333827080
> email: raffaele.calogero@unito.it
>      raffaele[dot]calogero[at]gmail[dot]com
> www:   http://www.bioinformatica.unito.it
> Info: http://publicationslist.org/raffaele.calogero
>
>

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