LDA/PCoA update

[akshayparopkari]

• LDA
  • Remove --input_data_type parameter.
  • utilize argparse checks for relevant input files for bubble plots.
  • Consolidate figure sizes for LDA and LDA bubble plots.
  • Add optional 3D plotting functionality.
• PCoA
  • allow users to input distance matrices for PCoA plotting purposes.
  • transfer PCoA computation to PhyloToAST backend.
  • allow users to calculate a variety of beta diversity metrics for downstream analysis.
  • add a parameter which lists out all the available beta diversity metrics which users can use.

[akshayparopkari]

LDA changes fixed in #59

[akshayparopkari]

Robust 3D LDA visualization capability added in #68