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

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

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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