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From: Vaneet L. <van...@uc...> - 2021-09-09 20:34:39
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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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From: Vaneet L. <van...@uc...> - 2021-09-13 16:06:33
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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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From: Colin <col...@gm...> - 2021-09-09 22:30:42
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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* > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Colin <col...@gm...> - 2021-09-09 22:35:02
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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*
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
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From: Vaneet L. <van...@uc...> - 2021-09-10 17:13:52
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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...<mailto: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...<mailto: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
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
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From: Colin <col...@gm...> - 2021-09-10 20:45:49
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>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* > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > |
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From: Vaneet L. <van...@uc...> - 2021-09-10 21:44:50
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Ok, that's what I thought, just checking. That is an interesting tool Biodalliance has, seems to be what we're trying to recreate...more or less. Thanks, Vaneet ________________________________ From: Colin <col...@gm...> Sent: September 10, 2021 2:45 PM To: Vaneet Lotay <van...@uc...> Cc: gmod-ajax <gmo...@li...> Subject: Re: [Gmod-ajax] Show labels in collapsed displayMode? [△EXTERNAL] >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...<mailto: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...<mailto:col...@gm...>> Sent: September 9, 2021 4:34 PM To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>> Cc: gmod-ajax <gmo...@li...<mailto: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...<mailto: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...<mailto: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 _______________________________________________ Gmod-ajax mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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