Re: [Gmod-ajax] Basic question: force labels on dense tracks JBrowse1?

[Scott C. <sc...@sc...>]

And I should have added, this is covered here:

https://jbrowse.org/docs/mouse_configs.html



On Mon, Mar 29, 2021 at 12:14 PM Scott Cain <sc...@sc...> wrote:

> Hi Hans,
>
> This one is pretty easy; you need the "unsafe" options:
>
> "unsafePopup" : true,
> "unsafeMouseover" : true,
>
> In your example, the popup one should do the trick.
>
> On Mon, Mar 29, 2021 at 11:03 AM Hans Vasquez-Gross via Gmod-ajax <
> gmo...@li...> wrote:
>
>> Also, is there a new setting to get html encoded in trask.conf or plugins
>> to render?  Here is an example using metadata.
>>
>> [ tracks.syn_a1hq ]
>> storeClass     = JBrowse/Store/SeqFeature/VCFTabix
>> urlTemplate    = syn/syn-wt_A-1.snpEff.highQ.vcf.gz
>> category = VCF / Syn Ab
>> #type = JBrowse/View/Track/CanvasVariants
>> type = VariantEffectPlugin/View/Track/CanvasEffectVariants
>> style.labelScale = 0.01
>> metadata.SNP-Colors = <span style='background-color:red'>&nbsp;</span>
>> <span style='color:red'>(Red)</span> - SNPs with truncations<br><span
>> style='background-color:purple'>&nbsp;</span> <span
>> style='color:purple'>(Violet)</span> - amino acid changes<br><span
>> style='background-color:green'>&nbsp;</span> <span
>> style='color:green'>(Green)</span> - silent mutations<br><span
>> style='background-color:blue'>&nbsp;</span> <span
>> style='color:blue'>(Blue)</span> - outside gene regions
>> key  = A-1 SnpEff HQ Variants
>>
>>
>> [image: Screen Shot 2021-03-29 at 11.01.38 AM.png]
>>
>>
>> On Mon, Mar 29, 2021 at 9:02 AM Hans Vasquez-Gross <
>> hav...@uc...> wrote:
>>
>>> Hi Colin,
>>>
>>> When we get our new webserver, I'll be setting it up so that we will
>>> have a public instance. For now though, it requires connecting via
>>> university VPN to load the website.
>>> Here is a screenshot of the track config of the M-10 Variant
>>> (non-labeled).
>>>
>>> [image: Screen Shot 2021-03-29 at 8.58.45 AM.png]
>>>
>>>
>>> Best,
>>> -Hans
>>>
>>>
>>>
>>> On Sun, Mar 28, 2021 at 10:57 PM Colin <col...@gm...> wrote:
>>>
>>>> The attribute style.labelScale=0.01 should be able to be used for
>>>> forcing VCF labels to be drawn on dense tracks (e.g.
>>>> https://jbrowse.org/docs/faq.html#my-track-doesn-t-display-the-gene-names-but-i-expected-it-to-why-not
>>>> )
>>>>
>>>> The value 0.01 corresponds to forcing labels to be drawn when you are
>>>> zoomed in closer than about 100,000bp view window or so (e.g.
>>>> 1000px/0.01pxPerBp=100,000bp)
>>>>
>>>> If you have an instance we can see that can be seen or any custom
>>>> config, maybe that would help?
>>>>
>>>> -Colin
>>>>
>>>> On Fri, Mar 26, 2021 at 8:07 PM Hans Vasquez-Gross via Gmod-ajax <
>>>> gmo...@li...> wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I want to force labels on VCF tracks. I found this on a previous
>>>>> email:
>>>>>
>>>>> "style":{"labelScale": 0.01}
>>>>> However, I dont use trackList.json for my VCF configurations, I use
>>>>> tracks.conf. I tried setting it as style.labelScale = 0.01, but the labels
>>>>> are still not being drawn on the track for dense tracks.
>>>>>
>>>>> Thank you,
>>>>> -Hans
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> Gmo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>
>>>>
>>>
>>> --
>>> Hans Vasquez-Gross
>>> <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross>
>>> PhD Candidate
>>> Dubcovsky Website - http://dubcovskylab.ucdavis.edu/
>>> Department of Plant Science
>>> University of California at Davis
>>> Email: hav...@uc...
>>> Skype: hansvg.ucd
>>>
>>
>>
>> --
>> Hans Vasquez-Gross
>> <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross>
>> PhD Candidate
>> Dubcovsky Website - http://dubcovskylab.ucdavis.edu/
>> Department of Plant Science
>> University of California at Davis
>> Email: hav...@uc...
>> Skype: hansvg.ucd
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research