LDA updates

[akshayparopkari]

Description

• Updated LDA.py
  • Moved bubble plot calculation and plotting to LDA_bubble.py script.
  • Updated package imports and import error check.
  • Removed get_relative_abundance() function.
  • Relative abundance is computed using PhyloToAST util module.
  • Expanded plot_LDA() function to accommodate new input parameters.
  • Added 3D plotting capability and X and Y axis label checks for variance calculations.
  • Reorganized and updated input parameters.
  • Updated input file error handling.
  • Script is compatible with Python 2 and Python 3 syntax.
  • Updated LDA script command line description.
  • Generalized distance matrix help message.
  • Updated documentation file for LDA.py script.
  • Added LDA_bubble script to visualization page in documentation.
• Added LDA_bubble.py
  • Split old LDA.py script into LDA.py and LDA_bubble.py.
  • Error handling for explained variance calculation and, consequently, plot X and Y axis labels added, in addition to input file error checks.
  • LDA_bubble.py is compatible with both Python2 and Python3.
  • Added documentation file for LDA_bubble.py script.
  • Added LDA_bubble script to complete script list page.
  • Generalized distance matrix help message.

Motivation and Context

Addresses #47 wrt changes in LDA.

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.