Menu
▾
▴
Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
|
From: Garrett S. <ste...@gm...> - 2022-08-04 21:51:14
|
Hi Chen,
I think it has to do with what you are coloring. In the ArcRenderer, the
arc is based on the top-level parent feature (e.g. a gene) where in the
SvgFeatureRenderer you are coloring a child feature (e.g. an mRNA), so you
have to retrieve the parent feature that has the itemRgb first.
Best,
Garrett
On Wed, Aug 3, 2022 at 8:54 PM Chen Xie <xi...@ev...> wrote:
> Hi Garrett,
>
> Thank you very much for your help! The problem is solved, but a bit
> different.
>
> For ArcRenderer, "color": "jexl:get(feature, 'itemRgb')" works, but
> "color": "jexl:get(parent(feature), 'itemRgb')" gives errors: "TypeError: e
> is undefined" for Firefox, and "TypeError: Cannot read properties of
> undefined (reading 'get')" for Chrome. However, for SvgFeatureRenderer (in
> the case of LinearBasicDisplay), "color1": "jexl:get(parent(feature),
> 'itemRgb')" works. Do you know the reason?
>
> Best wishes,
> Chen
>
>
>
>
> ----- 原始邮件 -----
> 发件人: "Garrett Stevens" <ste...@gm...>
> 收件人: "Chen Xie" <xi...@ev...>
> 抄送: "gmod-ajax" <gmo...@li...>
> 发送时间: 星期四, 2022年 8 月 04日 上午 8:33:36
> 主题: Re: [Gmod-ajax] About coloring tabix-indexed BED or bigBed tracks
>
> I might be able to help with this. The format of the arc renderer is
> different, so you'd have to have something like this for that display:
>
> {
> "type": "LinearArcDisplay",
> "displayId": "K562_bulk_co_sites_arc_color",
> "renderer": {
> "type": "ArcRenderer",
> "color": "jexl:get(parent(feature), 'itemRgb')"
> }
> }
>
> Note the different renderer type and "color" instead of "color1".
>
> Hope that helps,
> Garrett
>
> On Tue, Aug 2, 2022 at 11:01 PM Chen Xie <xi...@ev...> wrote:
>
> > 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
> > > > >
> > >
> >
> >
> > _______________________________________________
> > Gmod-ajax mailing list
> > Gmo...@li...
> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >
>
|
){kind=link}