Re: [Gmod-ajax] Colour reads from a BAM file

[Mitch S. <mit...@be...>]

  The current plan for this is to allow the user to specify a javascript 
function that gets called when features get put on screen, and can 
change the CSS style of a feature based on the feature data (which could 
include the ID, or whatever other information is in the JSON.

I've been experimenting with this lately; for example, in 
ucsc-to-json.pl there's a bit of perl that specifies a javascript 
callback, but it will be possible to specify that on the command line 
for flatfile-to-json.pl or in a config file for biodb-to-json.pl:

==========
     my $color = sprintf("#%02x%02x%02x",
                         $track->{colorR},
                         $track->{colorG},
                         $track->{colorB});

     if ($subfeatures) {
         $style{subfeatureHeaders} = \@subfeatHeaders;
         $style{class} = "generic_parent";
         $style{clientConfig}->{featureCallback} = <<ENDJS;
function(feat, fields, div) {
     if (fields.type) {
         div.className = "basic";
         switch (feat[fields.type]) {
         case "CDS":
         case "thick":
             div.style.height = "10px";
             div.style.marginTop = "-3px";
             break;
         case "UTR":
         case "thin":
             div.style.height = "6px";
             div.style.marginTop = "-1px";
             break;
         }
         div.style.backgroundColor = "$color";
     }
}
ENDJS
     }
==========

Currently, the callback gets the feature data, the "fields" object that 
specifies what's in the feature data, and the actual HTML element that 
will represent the feature.  That's not necessarily the final interface, 
but it's what I'm currently experimenting with.

This option should make it into the next release in December, but for 
now it's just work-in-progress.  On the plus side, if you have opinions 
about how it should work, now's your chance to weigh in :)

Mitch

On 10/08/2010 04:09 AM, James Casbon wrote:
> I'd like to see this as well.  My preference would be to assign
> colours based on the read group annotations in the BAM file.
>
> On 8 October 2010 11:52, James Morris<jm...@sa...>  wrote:
>> Hello,
>>
>> I am using Jbrowse to view some RNAseq data just on my local machine.
>>
>> Is it possible to colour the reads in a single track differently based on information I have in the id.
>>
>> I have 256 different classes (based on a 4bp sequence) so simply creating separate tracks for each class would not work as there would be too many tracks to view at once.
>>
>> If I could colour the reads I think it will be easy to visualise the distribution of the different classes at points where the reads pileup.
>>
>> Any help on this would be great.
>>
>> Thanks,
>>
>> James
>>
>> --
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> ------------------------------------------------------------------------------
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> experiences on the web. Be a part of the beta today.
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