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

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

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
> >
> >
> >
> >
> >
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> >