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Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
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From: Chen X. <xi...@ev...> - 2022-08-03 05:00:40
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Hi Colin,
Thank you very much for your quick reply! Your suggestion works, but not completely. If I do not add color configuration, such as:
"displays": [
{
"type": "LinearArcDisplay",
"displayId": "K562_bulk_co_sites_arc_color"
},
{
"type": "LinearBasicDisplay",
"displayId": "K562_bulk_co_sites_basic_color",
"renderer": {
"type": "SvgFeatureRenderer",
"color1": "jexl:get(parent(feature), 'itemRgb')"
}
}
],
It works. But when I add color configuration, it does not work. For example:
"displays": [
{
"type": "LinearArcDisplay",
"displayId": "K562_bulk_co_sites_arc_color",
"renderer": {
"type": "SvgFeatureRenderer",
"color1": "jexl:get(parent(feature), 'itemRgb')"
}
},
{
"type": "LinearBasicDisplay",
"displayId": "K562_bulk_co_sites_basic_color",
"renderer": {
"type": "SvgFeatureRenderer",
"color1": "jexl:get(parent(feature), 'itemRgb')"
}
}
],
I tried with both v1.7.10 and v2.1.0. Could you please help me on this? 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: 星期二, 2022年 8 月 02日 下午 7:10:33
主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
Hi there, there was a bug in the v2.0.0 release that caused this issue, we
will have it fixed in the next release
https://github.com/GMOD/jbrowse-components/pull/3120
To hardcode a displaytype as the default, it can be listed as first in the
"displays" array in the config, example:
{ "type": "FeatureTrack", "trackId": "gff3tabix_genes", "name": "GFF3Tabix
genes", "assemblyNames": [ "volvox" ], "adapter": { "type":
"Gff3TabixAdapter", "gffGzLocation": { "uri": "volvox.sort.gff3.gz" },
"index": { "location": { "uri": "volvox.sort.gff3.gz.tbi" } } },
"displays": [
{ "type": "LinearArcDisplay", "displayId":
"gff3tabix_genes-LinearArcDisplay" }, { "type": "LinearBasicDisplay",
"displayId": "gff3tabix_genes-LinearBasicDisplay" } ] }
-Colin
On Mon, Aug 1, 2022 at 9:05 PM Chen Xie <xi...@ev...> wrote:
> Hi Colin,
>
> Thank you for helping us on coloring tabix-indexed BED tracks. Here is a
> related question. The JBrowse version we set up before was 1.7.10, and now
> I notice that the lastest version is 2.1.0. However, when I upgraded our
> JBrowse to 2.1.0, LinearArcDisplay did not work anymore, i.e., nothing
> happened when I clicked "LinearArcDisplay". The reason that I would like to
> upgrade and try LinearArcDisplay for tabix-indexed BED tracks is as you
> mentioned, coloring tracks in LinearArcDisplay might be possible in the
> newer versions. Thus, could you please also show me how to config this in
> the "config.json" file? Thanks again!
>
> Best wishes,
> Chen
>
>
>
>
> ----- 原始邮件 -----
> 发件人: "Chen Xie" <xi...@ev...>
> 收件人: "Colin" <col...@gm...>
> 抄送: "gmod-ajax" <gmo...@li...>
> 发送时间: 星期五, 2022年 6 月 24日 下午 4:02:57
> 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
>
> Hi Colin,
>
> It works! Thank you very much, and look forward to your updates on
> LinearArcDisplay and bigInteract in future.
>
> 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: 星期五, 2022年 6 月 24日 下午 2:07:36
> 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
>
> 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...
> > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> > >
>
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