From: Louis L. <lou...@ma...> - 2009-09-30 02:08:33
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Coding is not a problem :-) I found the discussion after posting this. The FeatureTrack will do the trick for me I think. As for other browsers, I was told by a collegue that their might be a way on the UCSC browser to do this. When uploading a wiggle track you can choose to plot points instead of generating tracks. I haven't done it yet, and I prefer the smoothness of jbrowse by far, so I'll get it to work on it anyhow. I'm a bit of a new user to jbrowse (I played with an older version of gmod-ajax before though). Thanks alot for the quick answer! Louis Mitch Skinner wrote: > Louis Letourneau wrote: >> How would one go about creating a track which contains a 2D dot plot of >> data like log r ratios or b allele frequencies. >> >> These go from 0 to 1 and I would have 1 per snp in a dataset. >> > > So you want to have a 2D plot associated with each feature in a dataset, > right? I think it would take some work. You should be able to do this > once we implement per-feature callbacks in FeatureTrack, like we've been > discussing on the mailing list today in the "Using multiple glyphs per > track" thread. Then in one of those callbacks you can associate a 2D > plot image (which you would probably have to generate yourself; there's > nothing currently in JBrowse that will do this) with the feature. And > we'd have to implement a way for your callback to tell the FeatureTrack > code about the size and placement of the plot so that it can be laid out > properly. > > So the ability to do this is a little way in the future (a few weeks > maybe?). And you would probably have to do some coding of your own to > generate the plots and integrate them into the JBrowse view, although > arguably JBrowse should build in some of this functionality. > > Are there genome browsers that currently do this, that we could look at > as models? > > Mitch |