.. |pair_csv| image:: _static/pair_csv_example.png
.. |sing_csv| image:: _static/singleton_csv_example.png
.. |combined| image:: _static/cluster_Spleen_1_combined-01.jpg
.. |discrete| image:: _static/cluster_Spleen_1_discrete-01.jpg
.. |sing_cmb| image:: _static/cluster_Spleen_1_singleton_combined-01.jpg
.. |sing_TPTN| image:: _static/cluster_Spleen_1_singleton_TP_TN-1.jpg
.. |TPTN| image:: _static/cluster_Spleen_1_TP_TN-1.jpg

Examples
==========

Following is an example of COMET usage and output on the command line:

.. code-block:: none
		
    $ hgmd input/ output/
    Started on 2018-11-01T22:55:15.243954
    Reading data...
    Generating complement data...
    ########
    # Processing cluster 1...
    ########
    Running t test on singletons...
    Running XL-mHG on singletons...
    Creating discrete expression matrix...
    Finding pair expression matrix...
    Running hypergeometric test on pairs...
    Finding simple true positives/negatives for singletons...
    Finding simple true positives/negatives for pairs...
    Pickling data for later...
    Exporting cluster 1 output to CSV...
    Drawing plots...
    Drawing discrete plots...
    Drawing combined plots...
    Drawing singleton combined plots...
    Drawing true positive/negative plots...
    ########
    # Processing cluster 2...
    ########
    Running t test on singletons...
    Running XL-mHG on singletons...
    Creating discrete expression matrix...
    Finding pair expression matrix...
    Running hypergeometric test on pairs...
    Finding simple true positives/negatives for singletons...
    Finding simple true positives/negatives for pairs...
    Pickling data for later...
    Exporting cluster 2 output to CSV...
    Drawing plots...
    Drawing discrete plots...
    Drawing combined plots...
    Drawing singleton combined plots...
    Drawing true positive/negative plots...
    ########
    # Processing cluster 3...
    ########
    Running t test on singletons...
    Running XL-mHG on singletons...
    Creating discrete expression matrix...
    Finding pair expression matrix...
    Running hypergeometric test on pairs...
    Finding simple true positives/negatives for singletons...
    Finding simple true positives/negatives for pairs...
    Pickling data for later...
    Exporting cluster 3 output to CSV...
    Drawing plots...
    Drawing discrete plots...
    Drawing combined plots...
    Drawing singleton combined plots...
    Drawing true positive/negative plots...
    Ended on 2018-11-01T22:56:28.103160

Following are examples of COMET output:

|pair_csv| *CSV output*

|sing_csv| *Singleton-only CSV output*

|combined| *Combined continuous/discrete plots*

|discrete| *Discrete plots comparing combinations/singletons*

|sing_cmb| *Singleton-only combined plots*

|TPTN| *True positive/negative plot*

|sing_TPTN| *Singleton-only TP/TN plot*



    
.. toctree::