Re: [Gmod-ajax] quantitative tracks

[Mitch S. <mit...@be...>]

On 08/14/2009 01:48 AM, ambrose andongabo (RRes-Roth) wrote:
>
> Hello Mitch,
>
>                  I used JBrowse to display some data for scientist in 
> my lab.  This is comment from one of the scientist
>
> "It seems to behave a bit better when I restart the session.  I note 
> that the browser seems to remember the settings of which tracks etc 
> are chosen
>

Yeah, I've also encountered JBrowse bugs that were helped by refreshing 
the page.  Most of those have been fixed; it would helpful for us if 
people could take a screenshot of any weirdness they see and send it to 
us, with information about their browser and browser version and OS.  
That'll make it easier to track down and fix any remaining bugs.

After you've taken a screenshot and sent us an email describing the 
problem (hopefully with an exact list of steps to reproduce it), though, 
refreshing the page will usually help.

> · I like the features so far -- the top level navigation seems v. 
> useful -- will it be possible to catch each end of the red bar and 
> stretch/shrink?
>

It's an interesting idea.  Currently, you can drag the red box to a 
different location, but you can't change its size by manipulating it 
directly.  Adding both mechanics (drag the box if you mousedown in the 
middle, and resize the box if you mousedown on the ends) is possible, 
but I think that might be confusing for the user if you get two 
different behaviors based on a few pixels difference in where the mouse 
comes down.

Of course, we could also just remove the current dragging mechanic and 
replace it with a resizing mechanic.  Resizing might be a more common 
operation than scrolling; it really depends on the user, though.  Is 
there something specific this user commonly does that would be easier to 
do by resizing the red box (as opposed to using the zoom buttons, or 
entering a base range in the text box)?

> · The track titles take up a lot of space and therefore make some 
> comparisons between tracks less easy. Could they be brought down and 
> possibly made optionally transparent?
>

I've avoided transparency in JBrowse because it can slow down scrolling 
(this is browser-, OS-, and hardware-dependent, though).  I suppose we 
could make the label font smaller, but this involves a tradeoff and 
different users (especially older users) will want that different ways.  
We'll keep this in mind for future changes, but right now there are a 
few things you can do:

One is to change the default font size in your web browser; JBrowse 
doesn't currently set the font size on anything because I wanted to 
respect the user's own settings.  Exactly how to do this varies; I've 
been meaning to write up a description of how to do it on different 
browsers and OSes.  On the machine I'm writing this on (firefox on 
linux), it's under Edit->Preferences, in the Content tab.

The other thing you can do is set up your own user CSS.  This is 
definitely more involved, and it requires you to read the JBrowse CSS 
and understand some of it, but it gives you a great deal of control over 
how JBrowse looks.  For firefox, creating a user CSS file is described here:
http://www.mozilla.org/unix/customizing.html#userContent

Specifically, you can add CSS for "div.track-label" (and, optionally 
"div.tracklist-label").  Then you can set font size, transparency, 
background color, padding, whatever you like.

Documenting this better is on the to-do list, but some of the CSS is 
going to get changed around (for example, I'm going to add a "jbrowse-" 
prefix to all the CSS classes) so I'm waiting until the code settles 
down a bit before documenting it.

> · We will ideally need the gene features colour-coded on the plots 
> (i.e. as I have below), as this really makes the interpretation so 
> much easier
>

We don't currently have code to do this, but you can render your own 
image track however you like, and incorporate those images into 
JBrowse.  You have to create a json file describing your image track 
(this gives the image tile width in pixels, and for each zoom level, it 
gives a URL prefix, height, and number of bases per image tile).  This 
isn't documented yet (it's ticket #27), but you can see how it works if 
you look in bin/wig-to-json.pl and src/wig2png.cc in the JBrowse 
distribution.

> · The scaling of individual tracks needs to be interactive. This would 
> require (i) baseline offset; (ii) switch between fixed range; variable 
> range and auto-fit range;
>

This is on the to-do list; I've added ticket #41:
http://jbrowse.lighthouseapp.com/projects/23792/tickets/41

Offset and fixed range should be pretty straightforward.  I can imagine 
a few different meanings for "auto-fit range", and it would be helpful 
to have a detailed description of what this means to you, and use case 
for where it would be useful.

> · Note that some datasets may be --ve to +ve, i.e. with x-axis 
> intersecting y at zero, but ranging from e.g. -1 to +1."
>

The current wiggle renderer handles this, but presenting the zero better 
is definitely on the to-do list.  If you want to add color-coding to a 
quantitative plot to indicate gene model boundaries, you're on your own 
for the moment, though.  If you can already create the plots, it should 
be reasonably straightforward to re-purpose them for JBrowse, and I'd be 
happy to answer questions about how to do that.

Regards,
Mitch