Re: [Gmod-ajax] JBrowse scale tracks together

[Vaneet L. <van...@uc...>]

Thanks for the tip, already have that plugin installed and it is the closest thing to my request so far.  However it would nice to just have it  so that you can graph bigwigs in the traditional bigwig XY plot format.  The multibigwig plugin does have an XYplot option but it has no legend for each track and graph color.  Also I mean to graph all tracks separately in their own track lines as opposed to graphing them all together on the same physical space.  This does work though as a good temporary measure until a new feature can be added to JBrowse.

Vaneet


Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

From: Ke Jiang [mailto:bio...@gm...]
Sent: Thursday, October 25, 2018 11:25 AM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse scale tracks together

Would this help?

https://github.com/elsiklab/multibigwig

On Thu, Oct 25, 2018 at 12:10 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello all,

I am wondering if there’s a feature or plugin in JBrowse that allows you to view bigwig tracks together in a group that will allow you to scale them together when viewing them in a browser.  When I say scale them together, I don’t necessarily mean they all have the same maximum value for their graphs, but that whichever scaling you choose (local, global, max,…) that it’s common among all tracks in the group.

I think this is greatly needed because unless you set each bigwig track to the same maximum scale manually, comparing tracks together which are locally or globally scaled can be tough as more often than not they have different scales for their Y axes.

So I’m not sure if there’s a way to make track groups like this for this purpose, if not, please add this request for the next JBrowse release if you feel this is necessary.

I really appreciate you adding the sorting of track categories, so impressed with how quickly you guys post new JBrowse releases as well as adding user requests.  I wouldn’t really begin to know how you can add a feature for custom sorting tracks within a category, but would that be possible to add in a future release somehow? Maybe an orderID of some sort perhaps?

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
716 ICT Building – University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

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