============
diversity.py
============
Calculate the alpha diversity of a set of samples using one or more metrics and output a kernal density estimator-smoothed histogram of the results.

.. code-block:: bash

    usage: diversity.py [-h] [-d DIVERSITY [DIVERSITY ...]] [--plot_title PLOT_TITLE] [--image_type IMAGE_TYPE] [--save_calculations SAVE_CALCULATIONS] [--show_significance] [--show_available_metrics] -m MAP_FILE -i BIOM_FP -c CATEGORY --color_by COLOR_BY -o OUT_DIR

Required arguments
-------------------
.. cmdoption:: -m MAP_FILE, --map_file MAP_FILE

    QIIME mapping file.

.. cmdoption:: -i BIOM_FP, --biom_fp BIOM_FP

    BIOM table file name

.. cmdoption:: -c CATEGORY, --category CATEGORY

    Specific category from the mapping file.

.. cmdoption:: --color_by COLOR_BY

    A column name in the mapping file containing hexadecimal (#FF0000) color values that will be used to color the groups. Each sample ID must have a color entry.

.. cmdoption:: -o OUT_DIR, --out_dir OUT_DIR

    The directory all plots will be saved to.

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

    show this help message and exit

.. cmdoption:: -d DIVERSITY [DIVERSITY ...], --diversity DIVERSITY [DIVERSITY ...]

    The alpha diversity metric. Default value is 'shannon', which will calculate the Shannon entropy. Multiple metrics can be specified (space separated). The full list of metrics is available at: http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html.

.. cmdoption:: --plot_title PLOT_TITLE

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

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

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

.. cmdoption:: --save_calculations SAVE_CALCULATIONS

    Path and name of text file to store the calculated diversity metrics.

.. cmdoption:: --show_significance

    Display significance testing results. The results will be shown by default.

.. cmdoption:: --show_available_metrics

    Supply this parameter to see which alpha diversity metrics are available for usage. No calculations will be performed if this parameter is provided.