network_plots_gephi.py
======================

Create network plots based on correlation matrix.

.. code-block:: bash

    usage: network_plots_gephi.py [-h] [-go GEXF_OUT] [-fp FIL_PCT] [-w STATS_OUT_FNH] biom_file mapping_file condition_column in_corr_mat cat_name

Required Arguments
-------------------

.. cmdoption:: biom_file

    The biom-format file.

.. cmdoption:: mapping_file

    Mapping file for reading sampleIDs and their groups.

.. cmdoption:: condition_column

    Column name in mapping file denoting the categories.

.. cmdoption:: in_corr_mat

    Correlation matrix file. The format for the tab-separated file should be: Category -> Variable -> by Variable -> Correlation

.. cmdoption:: cat_name

    Category to be plotted.

Optional Arguments
------------------

.. cmdoption:: -go GEXF_OUT, --gexf_out GEXF_OUT

    The directory to output the PCoA plots to.

.. cmdoption:: --scaling_factor SCALING_FACTOR

    Graph information written to this Graph Exchange XML Format file. This file can be input to Gephi.

.. cmdoption:: -fp FIL_PCT, --fil_pct FIL_PCT

    Specify the minimum value of correlation strength to display. By default, all correlations greater than or equal to 0.75 will be shown.

.. cmdoption:: -w STATS_OUT_FNH, --stats_out_fnh STATS_OUT_FNH

    Write out graph statistics - degree and betweenness centrality calculations for each node.

.. cmdoption:: -h, --help

    Show this help message and exit