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arq5x / scurgen

A tool for detecting patterns in genomic data with space filling curves
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Generalize HilbertGUI #16

Open daler opened 11 years ago

daler commented 11 years ago

Right now HilbertGUI is hard-coded to use 2 files. It would be nice to support arbitrary numbers of files and generate all the necessary sliders for the GUI on the fly.

For example, it would be cool to be able to load up a pile of ENCODE histone mod data and fade them in and out over each other interactively. Of course, then you run into the problem of not having enough colors in the rainbow, but that's a problem for later.

arq5x commented 11 years ago

Absolutely. It would be great to have N tracks loaded and then be able to click on a range in the HC and have it load a UCSC browser-style window displaying the individual feature from each track in that region. The latter would benefit from TABIX-ed files, but I don't see that as a big bottleneck, as bedtools and pybedtools can read TABIX'ed (GZIP) files anyway.

daler commented 11 years ago

metaseq handles this pretty well -- it'll plot BAM, bigWig, bigBed, or any tabixed interval files. Only downside (and it's minor) is the extra dependency to have tabix. But I bet most folks using this will have it installed anyway.

The trick will be factoring out just the useful plotting bits from metaseq. I think the best way will be to put that code into another general genomic plotting package that scurgen (and the rest of metaseq) can import.