Summary and visualization requests

[btmonier]

• Added new parameters to plogtGvcf():
  • mData and mVar
  • allows user to override default sample color option with categorical data
• Added new generic, numberOfHaplotypes():
  • returns the number of unique haplotypes found within each reference range or
    the total value found within a PHGDataSet object
• Added getters to PHGDataSet objects:
  • numberOfChromosomes()
  • numberOfSamples()
  • numberOfRefRanges()
• Changed functions and variables containing taxa to samples
  • e.g., numberOfTaxa() is now numberOfSamples()
• Format tweaks to HaplotypeGraph objects' show() method
• Added new function plotHaploCount():
  • Plots unique haplotype counts for all or given reference ranges
• Added new function plotHaploDist():
  • Plots unique haplotype distribution for entire PHGDataSet object
• Added relevant sections to documentation

[lynnjo]

Nice updates to rPHG2