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

[Hans Vasquez-G. <hav...@uc...>]

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