Re: [Gmod-ajax] Assistance with Jbrowse

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

Sure thing! Glad to help

I think the key is to set this value in the config on your REST API track

region_feature_densities=true


-Colin

On Mon, Nov 26, 2018 at 8:50 AM Shorter, Thomas <ts...@le...>
wrote:

> Hi,
>
>
> Thank you for your help previously, I managed to sort a lot of my issues
> out because of it.
>
>
> I have now moved onto generating custom/dynamic CanvasFeature tracks and I
> am using a rest API to supply the feature data. Is there a way to have
> CanvasFeature tracks display data from the API's (base)/stats/regionFeatureDensities/(refseq_name)
> endpoint?
>
>
> Many thanks,
>
>
> Tom
> ------------------------------
> *From:* Colin <col...@gm...>
> *Sent:* 08 November 2018 16:37:29
> *To:* Scott Cain
> *Cc:* Shorter, Thomas; gmo...@li...; he...@gm...
> *Subject:* Re: [Gmod-ajax] Assistance with Jbrowse
>
> 1. The glyph configuration is just glyph, not style->glyph
> 2. The height can be changed via a callback in style->height e.g. "style":
> { "height": "function(feat) { return feature.get('my_feat_height') || 10;
> }" } would return some GFF attribute my_feature_height
> 3. Set style.featureScale=1000 and it will never be able to zoom in as far
> as to display the features (zoom are represented as pixels per basepair)
>
> For histogram customizations I would recommend probably making a custom
> bigwig track for coverage and use the "summary histograms" feature
> http://gmod.org/wiki/JBrowse_Configuration_Guide#Configuring_Summary_Histograms
> this will give you more flexibility than the built in histograms generated
> by flatfile-to-json (I am assuming you are using this based on a thread
> posted recently?)
>
> Hope that helps
>
> -Colin
>
>
> On Thu, Nov 8, 2018 at 11:24 AM Scott Cain <sc...@sc...> wrote:
>
> Hi Tom,
>
> You can definitely do those things but I’m on my phone, so it’s hard to
> write out using this keyboard. I’ve CC’d the jbrowse mailing list so if I
> don’t get back to you today it’s likely that somebody else on the list
> will.
>
> Scott
>
>
> On Nov 7, 2018, at 9:42 AM, Shorter, Thomas <ts...@le...> wrote:
>
> Hi,
>
>
> I'm surrently looking at using Jbrowse to display SNP data within a
> website I'm working on.
>
>
> I don't have much experience with JavaScript and I'm having some trouble
> following some of the guides/what I want to do isn't covered.
>
>
> If you could answer a few of my questions I'd be most greatful!
>
>
> Firstly, how do I set the glyph type? I've tried changing style.glyph to
> diamond in both the .conf and .json and within the track config itself in
> the browser window but this doesn't seem to work but I'm pretty sure I saw
> a diamond glyph whilst looking through the code.
>
>
> Next I'd like to be able to change the height of a glyph/feature based on
> data within the 9th column of the gff imported, is this possible and how?
>
>
> I'd also like to be able to always have the histogram showing, even at the
> single base level and if possible to have the bin size set to 2-5% of the
> window (i'll have to play about with the exact number) or to the size of a
> single base, whichever is bigger.
>
>
> Many thanks!
>
>
> Tom
>
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