Scaling issues when using the wiggle_xyplot glyph on BigWigSet track

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Scaling issues when using the wiggle_xyplot glyph on BigWigSet track

John Portwood
Hello,

I have a BigWigSet track which consists of four subtracks. The track looks nice for the most part, but when the subtracks are overlapped in the semi-transparent view the scaling makes the plots look misleading.

For example, in the screenshot below you can see the max values for each scale are: 287, 992, and 373, 456. The different scales make all the plots look similar which is fine for this view, but it would be ideal if they could be autoscaled based on the highest value among all subtracks for the displayed region (i.e, for this region it would be ideal if all the scales had a max value of 992). Is such a task possible without setting an arbitrary "max_score"?  
Inline image 1

Now, the "Semi-transparent overlap" view would suit my preferences quite nicely if the overlap plots adopted the scale with the highest max value. However, this view chooses to use the 2nd highest scale (456 in this sample region). Thus, the resulting view looks misleading:

 Inline image 2

Using the "autoscale = chromosome" option fixes the scales for the most part, but in this dataset the values can reach as high as 8,000 which makes the plots look tiny for regions like this. So ideally I'd like to have the max value calculated into the scale based only on the region currently displayed. I'm not too familiar with BigWigs, but it seems one option would be to use a subroutine in the "max_score" conf variable, and have it return the highest max value among all the subtracks for a given region. Is such a thing possible for the Bio::DB::BigWigSet features?

Any advice would be greatly appreciative.

Thanks!
--
John Portwood
1028 Crop Genome Informatics Laboratory 
Iowa State University - USDA - ARS
Ames, IA 50010

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Re: Scaling issues when using the wiggle_xyplot glyph on BigWigSet track

Timothy Parnell
Hi John,

I think what you are asking is perfectly reasonable. However, I don’t think it can be simply done (you’ve already noted the workarounds that I would have normally suggested and implemented myself). You would have to dig into the code itself to work out the changes, and the principal developer who set this up has largely been absent from these parts for a while.

Tim

> On May 28, 2015, at 9:53 AM, John Portwood <[hidden email]> wrote:
>
> Hello,
>
> I have a BigWigSet track which consists of four subtracks. The track looks nice for the most part, but when the subtracks are overlapped in the semi-transparent view the scaling makes the plots look misleading.
>
> For example, in the screenshot below you can see the max values for each scale are: 287, 992, and 373, 456. The different scales make all the plots look similar which is fine for this view, but it would be ideal if they could be autoscaled based on the highest value among all subtracks for the displayed region (i.e, for this region it would be ideal if all the scales had a max value of 992). Is such a task possible without setting an arbitrary "max_score"?  
> <image.png>
>
> Now, the "Semi-transparent overlap" view would suit my preferences quite nicely if the overlap plots adopted the scale with the highest max value. However, this view chooses to use the 2nd highest scale (456 in this sample region). Thus, the resulting view looks misleading:
>
>  <image.png>
>
> Using the "autoscale = chromosome" option fixes the scales for the most part, but in this dataset the values can reach as high as 8,000 which makes the plots look tiny for regions like this. So ideally I'd like to have the max value calculated into the scale based only on the region currently displayed. I'm not too familiar with BigWigs, but it seems one option would be to use a subroutine in the "max_score" conf variable, and have it return the highest max value among all the subtracks for a given region. Is such a thing possible for the Bio::DB::BigWigSet features?
>
> Any advice would be greatly appreciative.
>
> Thanks!
> --
> John Portwood
> 1028 Crop Genome Informatics Laboratory
> Iowa State University - USDA - ARS
> Ames, IA 50010
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> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

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