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 > > [[alternative HTML version deleted]]