Since the plots produced by the fancyplotting.py module are on a log scale, zero values that find their way into the data produce NaN values that trip up matplotlib. This pull request includes a number of minor stylistic changes (some of which are important for the upcoming configuration file interface pull request) as well as a fix for that bug.
Some of the more important changes also included in this pull request are the following
A synonym optimize_bgfs is added for the plain optimize function in tracts.py. All the other optimization methods in tracts follow the convention of being named optimize_METHOD, so this change is in the interest of consistency. This consistency is also essential to the upcoming configuration file interface.
The chromosome selection algorithm in tracts.py required that the list of chromosomes be given as a list of strings. This doesn't make much sense since chromosomes are typically numbered, so integer values should also be accepted. The selection algorithm has been adjusted to allow strings as well as integers.
Since the plots produced by the
fancyplotting.pymodule are on a log scale, zero values that find their way into the data produce NaN values that trip up matplotlib. This pull request includes a number of minor stylistic changes (some of which are important for the upcoming configuration file interface pull request) as well as a fix for that bug.Some of the more important changes also included in this pull request are the following
optimize_bgfsis added for the plainoptimizefunction intracts.py. All the other optimization methods in tracts follow the convention of being namedoptimize_METHOD, so this change is in the interest of consistency. This consistency is also essential to the upcoming configuration file interface.tracts.pyrequired that the list of chromosomes be given as a list of strings. This doesn't make much sense since chromosomes are typically numbered, so integer values should also be accepted. The selection algorithm has been adjusted to allow strings as well as integers.