Re: [Gmod-ajax] Openlazlo

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

On Mon, 2007-06-04 at 10:15 +0100, Steve Taylor wrote:
> There are an increasing number of biological techniques that are
> producing genome wide quantitative data that require graph like
> visualisation, such as array intensities and ChIP-on-chip. While 
> graphs/plots *can* be broken down into rectangles how do think the div
> method will cope with the increased amounts of elements required?

This is a really good point that Ian and I have been talking about a
lot.  The consensus is that there's some density threshold above which
you'd have to use images.

Images fit well with that kind of dense quantitative data because:
1. there's no layout (bumping)
2. they can be very dense
3. As far as I know, there's no need to click on individual data points,
the way you'd click on individual features (and therefore no need for an
imagemap).  One of the nice things about using divs for feature tracks
is that a div's visual span is the same as its region of clickability,
so there's no need to specify that separately with something like an
imagemap.  But if there's no clicking then it doesn't matter.

Not needing layout (or text labels) for that kind of data makes it
easier to render images on demand, since there's no need to worry about
distant elements affecting the image tile that you're rendering.

Not having any text (or anything aspect-ratio dependent) in the image
tile also makes it possible to scale images on the client without making
them look odd.  We could just horizontally stretch out the
1-base-per-pixel image for higher zoom levels, which (if you were
pre-rendering) would save you a lot of disk space and processing time.
Or, if you were rendering on demand, some bandwidth and server CPU.

Also, I can't think of any reason you'd want to edit that kind of data
the way you might want to edit a feature.

Point being, feature tracks and measurement-type tracks are pretty
different animals IMO, and while divs are a good solution for feature
tracks, images are probably the right way to go for dense measurement
tracks.  So I think we'd want to have both image-based tracks and
div-based tracks side-by-side.  AFAICT this shouldn't be too hard.


That's the consensus as I see it; personally I think it's fine to
visualize ChIP/chip data with a bar graph where each bar is (say) 10
pixels wide, as long as it's easy to zoom in to see more detail.
Everyone I've talked to seems to think that's crazy, although no-one
seems terribly bothered by the fact that at low zoom levels (say, a
whole chromosome) even 1-pixel granular plots will still be averaging
over a large area for each visible data point.  What I'd like to see
(regardless of the image/div decision) are plots that show you not only
a mean but also a max and a min (or a standard deviation, or something)
for each plot point where averaging has been done.  Explicitly
acknowledge the fact that the visualization is coarse, in other words.
Then coarse visualizations become less scary.

That's all just my opinion, though.  I'm happy to implement whatever
image-based stuff people think is important.  I may be somewhat biased
about the div thing.

Mitch