Re: [Gmod-ajax] Show labels in collapsed displayMode?

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

>Thanks for those tips.  Can you tell me how the collapsed mode works?  For
example, when there are multiple mRNA models in normal mode that collapse
to one in collapsed mode, is it simply showing the longest possible
transcript with the union of all possible exon and inner segments?

It is not really doing anything intelligent, it simply plots all
transcripts at y-coordinate 0.

This is why in most cases, drawing labels and having mouseovers is a
non-sense behavior in collapsed mode. The ChromHMM track is a nice special
case where the collapsing gives a simple row of chromatin states though, so
mouseovers and clicks are manually added via config

There is perhaps a good need to make a smarter system. It is often
overwhelming for every gene to have all transcript isoforms displayed all
the time. Most people may be satisfied to show the union of possible
exon/inner segments. Biodalliance has a mode kind of like this (the genes
track when you visit here https://www.biodalliance.org/ has this enabled)


-Colin

On Fri, Sep 10, 2021 at 1:13 PM Vaneet Lotay <van...@uc...>
wrote:

> Hey Colin,
>
> Thanks for those tips.  Can you tell me how the collapsed mode works?  For
> example, when there are multiple mRNA models in normal mode that collapse
> to one in collapsed mode, is it simply showing the longest possible
> transcript with the union of all possible exon and inner segments?
>
> Vaneet
> ------------------------------
> *From:* Colin <col...@gm...>
> *Sent:* September 9, 2021 4:34 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmod-ajax <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] Show labels in collapsed displayMode?
>
> [△EXTERNAL]
>
> Also add
>
>             disableCollapsedClick: false,
>
> See https://github.com/GMOD/jbrowse/blob/master/setup.sh#L208
>
> for how this particular track is setup
>
> -Colin
>
> On Thu, Sep 9, 2021 at 6:30 PM Colin <col...@gm...> wrote:
>
> You can add a "enableCollapsedMouseover": true to get the right click on
> the collapsed tracks. The ChromHMM track in our volvox demo uses this
>
>
> https://jbrowse.org/code/JBrowse-1.16.11/?loc=ctgA%3A9881..32090&tracks=ChromHMM&data=sample_data%2Fjson%2Fvolvox&tracklist=1&highlight=&nav=1&overview=1
>
> I am not sure we have feature labels in collapsed mode but there is a
> mouseover
>
>
> -Colin
>
> On Thu, Sep 9, 2021 at 4:35 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello,
>
>
>
> Is there a way to show feature labels in collapsed displayMode? For a
> certain track that has many transcripts our group likes the way collapsed
> mode appears to shrink it down into one consensus gene model but of course
> since it’s collapsed the feature labels are gone, anyway to leave them on?
> Also I noticed the option menu when you right click on the feature in
> normal mode is gone from collapsed mode, is there any way to bring that
> option back when it’s collapsed so you can still right click on the feature
> to bring up those same options?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building – University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
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