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Re: [Gmod-ajax] JBrowse wiggle file display - png
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From: Shankar A. S. <sha...@gm...> - 2009-09-29 14:06:56
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Hi Mitch, I circumvented the problem by converting my data to a log scale (base 2), so the track looks like a set of jagged peaks that I expected to see. Looking through the code very briefly it appears as though that JBrowse precomputes png images for wiggle tracks at different zoom levels. If that's the case, you're absolutely right, it's a tough task to adjust the scale to values in the visible region (akin to the UCSC genome browser). The use case that you described (100 vs 200 and 100k vs 200k) both constitute interesting differences since there is a two-fold difference between the min and max for the two regions. In my particular case, if I were to compare two conditions/experiments (say, pre- and post-treatment) where a particular region varies between 1-500 (which is no doubt "interesting"), I'm unable to see this difference on the browser currently, since the threshold to have a data point displayed with my data range (1-200k) is ~1000. I suppose vertical scaling will help fix this. Correct me if I am wrong. I don't know if I answered your question, but I'd be happy to answer any further questions that you might have in making improvements. Regards, Shankar On Tue, Sep 29, 2009 at 5:51 AM, Mitch Skinner <mit...@be...> 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 > |
