GUI updates, bigWig support, docs, and more

daler commented 11 years ago

Big chunk o' commits, but I think the end result is a substantial improvement. The bigWig support speeds things up nicely since data are essentially pre-binned.

Summary of changes:

sphinx docs with custom template for autodocs and API summary tables
lots of docstrings to help make sense of things when returning to the code base after a few weeks . . .
use default chroms from pybedtools
support for bigWig (see HilbertMatrixBigWig class; use it by simply adding a bigwig=True to the data section of a config).
refactored HilbertGUI into HilbertPlot (which exposes all the knobs and dials as an API, useful for batch plotting) and HilbertGUI (which adds the GUI widgets to control said knobs)
colormap adjustments
precompute.py script which saves a compressed numpy array of precomputed d2rc coords
save() method now ignores GUI widgets
chromosome outlines (implemented as a contour)

Example of GUI using bigWig input, with chrom boundaries: example screenshot

arq5x commented 11 years ago

Looks like a fantastic addition! I merged but can't run because I don't have bx.bbi.bigwig_file. Do you know what should be added to setup.py to auto-install this?

arq5x commented 11 years ago

I added bx-python to setup.py and am in business. Pushed to repo.

arq5x commented 11 years ago

It looks like precomputed.npz is not installed - I get a IOError: [Errno 2] No such file or directory: '/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/scurgen-0.1.0-py2.7.egg/scurgen/precomputed.npz' message. Is this a static file that should be installed with the package?

arq5x commented 11 years ago

It looks like there is an expectation that the chrom2rc method is available in all HilbertMatrix* objects. I ran the GUI with a BED file as an input, but it failed when calling chrom2rc, which is present in the BigWig subclass. At first glance it seems that this method should be in the base class?

daler commented 11 years ago

I haven't figured out the best way to make precomputed.npz . . . I think ideally it would be when running setup.py upon first install. For now though, run precompute.py to make the .npz file.

daler commented 11 years ago

Ah right, I forgot that I used chrom2rc when making the chrom outlines. You're right, it's no longer bigWig-specific and should be in a base class

arq5x / scurgen

GUI updates, bigWig support, docs, and more #33