Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks

[Colin <col...@gm...>]

Small correction, you can actually specify the color callback for
LinearArcDisplay in the config.json in current versions, but it just isn't
visible as a callback in the UI

Will be fixed in next version now

-Colin

On Tue, Jun 21, 2022 at 12:02 PM Colin <col...@gm...> wrote:

> Hi Chen
> Great questions
>
> For the color callback, I think you have the right idea. The "field8"
> would be an autoassigned name if the columns of your bed file do not have
> names. If you have bigBed, you may have column names (they are often
> provided by an autoSql file). You can check the column names using
> bigBedInfo or the "About track" inside jbrowse 2. Then just swap out field8
> for whatever the column name is. Let me know if this still has issues
>
> For the other questions
>
> 1) Looks like currently LinearArcDisplay does not have a color callback,
> we will add this!
> 2) I think bigInteract would be a great thing to try to make an example of
> for our docs. I think if you wanted to, you could load a bigInteract bigBed
> file, and use LinearArcDisplay, and it would generally work. The features
> of bigInteract that would be missing are the  "feet" (e.g. the lines at
> each end of arc here
> https://genome.ucsc.edu/images/interactUnderstanding2.png) would be
> missing, and the interchromosomal indicators would not display
>
> -Colin
>
>
>
>
> On Tue, Jun 21, 2022 at 12:52 AM Chen Xie <xi...@ev...> wrote:
>
>> Dear Madam/Sir,
>>
>> We have installed your JBrowse 2 on our server to visualize our
>> sequencing data. Currently, we met a problem about coloring tabix-indexed
>> BED or bigBed tracks. We put RGB values at the 9th column, and tried by
>> following "https://github.com/GMOD/jbrowse-components/discussions/2561"
>> and "https://github.com/GMOD/jbrowse-components/discussions/2772", but
>> it did not work. Our configuration in "config.json" is similar to (we
>> tested with many small changes):
>>
>>       "displays": [
>>         {
>>           "type": "LinearBasicDisplay",
>>           "displayId": "color_test",
>>           "renderer": {
>>             "type": "SvgFeatureRenderer",
>>             "color1": "jexl:get(feature,
>> 'field8')=='255,0,0'?'red':'blue'"
>>           }
>>         }
>>       ],
>>
>> With the codes above, it always shows blue color, even when the itemRgb
>> column is '255,0,0', and we also tried with 'field9', but it did not work
>> either. I guess that we did not put the correct name of the feature there.
>> Could you please help us on it?
>>
>> Here are two further quesions:
>>
>> 1. It is great to have this "LinearArcDisplay" in JBrowse 2, can we also
>> color lines in this type of display?
>>
>> 2. We would like to visualize data in the format of UCSC interact ("
>> https://genome.ucsc.edu/goldenPath/help/interact.html"), which is
>> actually similar to your LinearArcDisplay. Do you plan to support it?
>>
>> Thank you very much and look forward to your reply!
>>
>> Best wishes,
>> Chen Xie
>>
>>
>>
>>
>>
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