Update scripts/collate_alpha.py

Update the collate alpha script to ignore directories. Empty directories can be left over from previous (interrupted) alpha_diversity.py run 
Update scripts/collate_alpha.py

Updates as per Greg's suggestion
Added support for empty distribution boxplots.

Support added at lower level distribution_plots.py code. Need to add tests and then work on make_distance_boxplots.py code to make sure that it will support empty distributions as well.
Updated existing distribution_plots.py tests.
Added tests for empty distributions and coloring.
Updated pairwise tests text to be clearer.
added function get_adjacent_coordinates

to address #766
added more tests
cleaned up code and tests
renamed based on input from @jrrideout
expanded on doc string
cleaned up some terminology
Merge pull request #767 from gregcaporaso/issue-766

fixes #766
Merge pull request #740 from jrrideout/issue_716

Added support for plotting empty distributions in box plots.
Merge pull request #659 from zachcp/patch-3

Update collate_alpha.py to avoid directories
updated to use change made in #741
updated to use default depth for compare_alpha_diversity.py

this is the second half of addressing #711 (where the first half was completed in #741)
Merge pull request #770 from gregcaporaso/issue-711

updated to use default depth for compare_alpha_diversity.py
reverting #659 - this isn't actually working for me
removed extra import