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Re: [Gmod-ajax] JBrowse wiggle file display - png
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From: Brenton G. <brg...@gm...> - 2009-09-29 14:33:17
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Hi Mitch, Sorry to delay in responding about the vertical scaling issues. As you mentioned in a previous email, there are issues with dynamic and static scaling whether on a linear or log scale. For instance, for some of our RNA-Seq datasets there are genes with hundreds of thousands of reads right next to a gene that is expressed at low levels. What linear scaling allows you to do is see the full range. In a case like this, log scaling would help, but with such a dynamic range, even the low expressed genes would be very low. The other thing about log scaling is that, at least to me, it is non-intuitive. The best thing would be something along the lines of what you mention - some type of "y-zooming". This way, if you are interested in low expression of a certain segment in a region that also contains highly expressed genes, you could see it by zooming in. Similarly, to see the real dynamic range, you could zoom out. Nonetheless, I'll make a few tracks with linear scaling with a limit of 100 or so, linear scaling using the real max, and a log scale track and send some screenshot/links. Cheers, Brent On Sep 29, 2009, at 6:51 AM, Mitch Skinner wrote: > The short answer is; right now you can set the scale with the --min > and > --max command line parameters. > > Sometime soon, we'll be implementing a log scale option. Enabling the > user to zoom vertically is something I'd like to do; there's a basic > version of that that would be easy to implement (toggling between a > "full" and "compressed" vertical axis is what I have in mind). Would > any of those things help in your case? > > Implementing a vertical scale indicator is definitely on the to-do > list. > > Brenton Gravely has been advocating making the vertical scale adjust > to > the values in the visible region; I think that would be hard to > implement so it's probably not going to happen near-term unless > someone > wants to tackle it. > > I only have a basic understanding of exactly what people are using > RNA-seq for. So I'd like to know: in your case, how does the data > answer a biological question? If (say) one region has variation > between > 100 and 200, and another region has variation between 100,000 and > 200,000, are the 100-200 differences and the 100k-200k differences > both > interesting? In other words, what constitutes meaningful variation > your > RNA-seq data? > > I keep asking these questions, and so far I haven't gotten an answer > that has made it clear for me. Maybe we're at an exploratory stage > where the answers aren't clear in general? I don't know. It's > tough to > make good UI decisions if the use case isn't clear. > > Mitch > > On 09/28/2009 01:24 PM, Shankar Ajay Subramanian wrote: >> Hi, >> >> I'm a newbie to JBrowse and I was wondering if someone could help me >> out with my question. I currently have a de novo genome assembly on >> which I'd like to overlay wiggle tracks from RNA-seq data. The wiggle >> file (variableStep) has values that are in the range 1-275000. This >> (huge) range of values is probably why most of the regions appear to >> be without any reads/expression - the low values are probably not >> rendered in the png image. >> >> I'm wondering if there's a solution to see the data at a better >> resolution/scale. Are there options while converting to json that I >> can use to make it appear better? Is dynamic scaling possible as a >> user zooms in/out? Or should I do my own scaling/transposition before >> I do the json conversion? >> >> Thanks, >> Shankar >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry® Developer Conference in SF, >> CA >> is the only developer event you need to attend this year. Jumpstart >> your >> developing skills, take BlackBerry mobile applications to market >> and stay >> ahead of the curve. Join us from November 9-12, 2009. Register >> now! >> http://p.sf.net/sfu/devconf >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry® Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9-12, 2009. Register > now! > http://p.sf.net/sfu/devconf > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
