Re: [Gmod-ajax] JBrowse feature requests

[Mitch S. <mi...@ar...>]

To add a little bit to what Ian said:

Fabrice David wrote:
> Zooming in/out dynamically in the web browser would require to 
> generate images for the different levels... As a suggestion, would it 
> be possible to create JSON (transformed into SVG in the browser) 
> instead of an image; like for the gene density view? Then, users could 
> custom both the resolution (bin size), scale and range dynamically. 
> But I guess there is a problem of performance doing this way?

Yes, the reason we're using pre-rendered images is for performance, and 
also to support Internet Explorer (which doesn't have SVG).  The web 
browser is able to scale (and offset) pre-rendered images on the client 
side though, which is something I'd like to implement at some point.  
But that scaling couldn't switch between log and linear scales.

> In the case of superposed tracks, we should probably avoid confusion 
> having multiple scales; and assume that values in the different tracks 
> are directly comparable. Then, indeed, if the different tracks have 
> not the same scale/range, we should notice it easily having 
> superimposed and unreadable scales. But, this is less true for the 
> type of display (if we use the min or the max to display the histogram 
> - ticket #35). Then we could be comparing tracks that are actually not 
> comparable. Thus, it should be probably useful to set constraints 
> about which tracks can be superposed in TrackInfo.js. Following these 
> constraints people could superimpose or not tracks by drag-and-drop.

Well, I could imagine data sources with different scales that you might 
want to compare.  Say, comparing microarray expression data with RNA-seq 
expression data, maybe.  I don't know if people would really want to do 
that, but I do think that people might want to compare tracks with 
different scales.  My main concern is about how those differences ought 
to be reflected in the user interface.

I think we can wait until we start implementing this functionality to 
make some of these decisions, though.

> However, there is still a problem about superimposing several images: 
> the z-index matters. As Bernhard proposed, you could use 
> semi-transparency for the foreground, and/or maybe also add another 
> option to render the tracks as single lines instead of histograms; 
> allowing the comparison of more than 2 tracks. What do you think about 
> this?

Yes, the z-index matters, but setting the z-index should be do-able, 
although it might require some changes to the way ImageTrack.js.  Or 
maybe I'm misunderstanding the problem you're talking about?

One issue will be semi-transparency support in IE 6; we'll have to do 
some experiments to see what (if anything) works there.

By "render the tracks as single lines instead of histograms", you mean 
using color to indicate the quantitative value?  That's definitely high 
on the to-do list (ticket #7).  That will probably get done before 
superimposing tracks.

Mitch