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

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

We also have considered making it use itemRgb field for coloring by default
too, if interested you can check out
https://github.com/GMOD/jbrowse-components/issues/1734

-Colin

On Fri, Jun 24, 2022 at 12:07 AM Colin <col...@gm...> wrote:

> If I am reading the screenshot correctly, this is helpful to see.
>
> The reason for the issue you are seeing is because jbrowse "synthesizes
> child features" from the bigBed feature, and so you would actually want to
> access the parent feature's itemRgb field.
>
> Here is an example
>
> get(parent(feature),'itemRgb')
>
> This get's the parent feature's itemRgv field. Another helpful thing for
> debugging you can try is
>
> get(parent(log(feature)),'itemRgb')
>
> This is exactly the same as above, but it console.log's the feature so you
> can inspect it in the chrome devtools :)
>
> Potentially we could transfer the parent feature data fields onto the
> child feature to help with this case, or make a utility function that
> automatically looks at current and parent feature or something like that.
> Hope that helps though!
>
>
> -Colin
>
> On Thu, Jun 23, 2022 at 11:01 PM Chen Xie <xi...@ev...> wrote:
>
>> Hi Colin,
>>
>> Thank you very much for your nice reply! But after trying a lot in the
>> past days, I still have the same problem. As the example you can see in the
>> attached picture, everything is blue including the ones should be red. The
>> collumn name must be correct because I also tested with mouse over (see the
>> red rectangels). Could you please help me to figure out the reason? Thanks
>> again!
>>
>> Best wishes,
>> Chen
>>
>>
>>
>>
>> ----- 原始邮件 -----
>> 发件人: "Colin" <col...@gm...>
>> 收件人: "Chen Xie" <xi...@ev...>
>> 抄送: "gmod-ajax" <gmo...@li...>
>> 发送时间: 星期三, 2022年 6 月 22日 上午 2:02:04
>> 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
>>
>> 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
>> >
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > Gmod-ajax mailing list
>> > Gmo...@li...
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>> >
>
>