PCoA updates

[akshayparopkari]

Description

• PCoA_bubble.py:
  • Removed get_relative_abundance() function in favor of PhyloToAST in built function in biom_calc.
  • Plot legends will not use matplotlib’s Rectangle patch.
  • Axis labels updated to be consistent with LDA scripts.
  • Default scaling factor reduced by 10 fold, for clarity in plots.
  • This script has Python2 as well as Python3 compatible syntax.
• PCoA.py:
  • Updated imports to conform with PEP8 style.
  • Plot legends will not use matplotlib’s Rectangle patch.
  • This script has Python2 as well as Python3 compatible syntax.

Motivation and Context

• Consolidating figure outputs across all beta diversity scripts.
• Making scripts compatible with Python3 syntax.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.

[smdabdoub]

PCoA.py and PCoA_bubble.py now python 3 compatible (#50).

[akshayparopkari]

Minor update in PR #61