Re: [Gmod-ajax] local autoscale for coverage depth in Alignments2 tracks

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

The coverage that is displayed using the histograms is implemented
differently from a normal XYPlot, so there is less configuration available.
But what does happen is that it gets "stats" from the bigwig store if you
have the bigwig histogram configured, and then uses "stats.max" so it
should be similar to autoscale=global. That "stats.max" is different for
each refseq. If you want it the same globally across all refseqs you can
manually set "histograms.max" in the config

-Colin

On Mon, Oct 1, 2018 at 10:51 AM Loraine Guéguen <
lor...@sb...> wrote:

> But how is set the default scale for he coverage depth histogram of the
> Alignments2 track ? "autoscale"="global" ?
> It seems to depend on the data (different scale for different track) but
> not on the zoom level.
>
>
>
> Le 01/10/2018 09:42, Loraine Guéguen a écrit :
>
> ok, I have added a comment in the GitHub issue.
> Thanks
>
> Le 30/09/2018 16:48, Colin a écrit :
>
> The only thing I can really say is to stay tuned to the GitHub issue :) If
> it has a github issue that has stayed open it is likely still on our radar
>
>
> -Colin
>
> On Fri, Sep 28, 2018 at 11:28 AM Loraine Guéguen <
> lor...@sb...> wrote:
>
>> Dear JBrowse team and list,
>>
>> The same Bigwig file in a track of type XYPlot and in a track of type
>> Alignments2 (BAM display) with the coverage depth histogram is not
>> displayed with the same scale. Whereas the scale in the XYPlot track
>> looks fine (with autoscale=local), the scale in the coverage depth of
>> the Alignments2 track is not suitable (too big).
>>
>> How is set the display scale for the coverage depth of the Alignments2
>> track ?
>> I would like to set "autoscale"="local" as in XYPlot tracks, but it
>> seems it is not working (because of
>> https://github.com/GMOD/jbrowse/issues/1164#issuecomment-410875923 ?)
>>
>> Thanks,
>>
>> Loraine Guéguen
>>
>> --
>> Loraine Guéguen
>>
>> UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
>> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
>>
>> Station Biologique de Roscoff - CNRS | Sorbonne Université
>> Place Georges Teissier - CS 90074
>> 29688 Roscoff cedex
>> tel: ++33 (0)2 98 29 56 46 (interne : 415)
>> http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
>> http://abims.sb-roscoff.fr/
>>
>>
>>
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>>
>
> --
> Loraine Guéguen
>
> UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
>
> Station Biologique de Roscoff - CNRS | Sorbonne Université
> Place Georges Teissier - CS 90074
> 29688 Roscoff cedex
> tel: ++33 (0)2 98 29 56 46 (interne : 415)http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-modelshttp://abims.sb-roscoff.fr/
>
>
>
>
>
> _______________________________________________
> Gmod-ajax mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> --
> Loraine Guéguen
>
> UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
>
> Station Biologique de Roscoff - CNRS | Sorbonne Université
> Place Georges Teissier - CS 90074
> 29688 Roscoff cedex
> tel: ++33 (0)2 98 29 56 46 (interne : 415)http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-modelshttp://abims.sb-roscoff.fr/
>
>