============
diversity.py
============
Calculate and plot for two sample categories: Shannon diversity, Chao1 diversity, and a Jaccard similiarity distance matrix heatmap.

.. code-block:: bash

    usage: usage: diversity.py [-h][-c {shannon,chao1,jaccard} [{shannon,chao1,jaccard} ...]] [-p IMAGE_TYPE] map_file biom_file category plot_title out_dir

Required arguments
-------------------
.. cmdoption:: map_file

    QIIME mapping file.

.. cmdoption:: biom_file

    BIOM table file name

.. cmdoption:: category

    Specific category from the mapping file.

.. cmdoption:: plot_title

    The name of a PDF file the pathway map will be written to.

.. cmdoption:: out_dir

    The directory all plots will be saved to.

Optional arguments
------------------
.. cmdoption:: -h, --help

    show this help message and exit

.. cmdoption:: -c {shannon,chao1,jaccard} [{shannon,chao1,jaccard} ...]

    Choose the type of calculation needed. Default value is "None", which will output all 3 types of calculations.

.. cmdoption:: -p IMAGE_TYPE, --image_type IMAGE_TYPE

    The type of image to save: PNG, SVG, etc.