Parallelize MakeComparisonFiles
Add option for stripping out a low rate of mapping

In my experience, this also tends to correlate well with shitty data for that
slice. Probably better to ignore it, or re-calculate the average based on
neighbors.
Use diagonal instead of crosshatching to indicate NaN

I found the crosshatching a little distracting, it doesn't work well with
varying slice widths since you sometimes don't see the full hatch, and it also
had trouble lining up in a consistent manner.
Add an 'absolute' earth-mover distance function

This should take into account changes in absolute levels.  In practice, it
seems to weight far too heavily on the changes in level, and too little on the
patterns
Refactoring, various plotting tweaks
Start on code to make comparison betweeen binding and fold-change in bcd genes

See daily notes for 5 september, 2014
Use box height for row labels, rather than box_size
Attempt at doing logistic fitting of fold-change vs binding

See daily notes on 8 September
Early attempts at fitting
Speed and accuracy tweaks to map-rate skipping
Tweaks ot MakeComparisonFiles

* Option to force making a low-expression image.
* Spun out more of the svg_call parameters to separate variables.
* Tweaked sizes for printing on business cards.
Additions to TotalBindingHeatmap

* Refactoring the generation of binding matrices.
* Attempts to make fits.
* Save all fits
Multitude of changes to WTZldBcdHistograms

* Refactor earth_mover_multi so it properly deals with replicates. Not sure yet
   if I actually deal with this right in the calling code, but that's okay.

* Add in a tweakable (small) weight on how much to weight total expression
   level change

* Plotting tweaks

* Plotting refactoring

* Better handling of low expression.

* Output refactoring (now just use pandas)
Tweaks to constants and plotting order
Merge branch 'master' into BcdRNAi

Conflicts:
	DistributionDifference.py
	MakeComparisonFiles.py
	Makefile
	WTZldBcdHistograms.py
	analyze.make
Add option for normalization

Based on the greatest distance from 0, this centers everything at 0.5, and is
useful for showing things that might be positive or negative.  Recommeded
colormaps include cm.RdBu, cm.PuOr, etc
Spin off binding data into BindUtils

This is in preparation for doing some very similar things from the PCA script
Code for doing WT-Zld-Bcd PCAs

See notes on September 23-24, 2014
make some basic attempt at not overfitting

what I've done here is split the data in half, then see how well
the two halves agree with each other
Tweaks for plotting on black background

Nothing to see here, move along!