build_communities_final.py -- master script
    1. Loads in input adjacency matrix found in 'data' folder
    2. Divides the network into communities
    3. Saves .jpg image to current directory of the color-coded communities 

girvan_newman_manual.py -- manually coded girvan_newman algorithm
    -- I had an issue with visualizing the output as it is a "generator" object. 
       I was having trouble accessing the data stores inside what should have been a tuple
       I plan to continue to look into this...
       
build_graph_scratch.py -- lays out my three different attempts to create the graph object
                           with the correct connectivity (all unsuccessful unfortunately)
      
slides.md -- markdown file that contains the presentation slides
    make_slides.py -- script that converts .md files into .html slides
    slides.html -- .html version of the slides

Notes:      I only split unto 2 communities here. Later I can easliy to more by modifying the input to girvan_newman function
            The project rubric wants docstrings. I include these in my 'girvan_newman_manual' file when defining my own functions
            This file will run, and I believe correctly, I just cannot access the output. 

Issues:     The connectivity of my current graph is messed up. The node positions seem to be correct, but the 
            edges clearly are not. It should look like more of a tesselation of polygon shapes that represent cells.

            I cannot for the life of me figure out why... When I create the graph in matlab from the adj_mat it works 
            just fine, so it's not the adjacency matrix itself. What it could be is the process of sacing the adj_mat
            to adj_mat.txt or how I am reading it in... (in matlab im not using the .txt file but the .mat file)
    
Successes:  I mean I was able to use girvan_newman to split into communities... but thats not all that difficult
            I just type a letter into a pre-defined function. LIke i said I wrote my own version which I am pretty
            damn sure works, but I have trouble actually accessing the output to visualize it...
           

Next Steps: Definitely fix the connectivity, then set up look to run successive time frames (super easy to do)
            and make a cute little color-coded video showing the dyamics of the network communities over time,
            and see how the communities might change over different phenotypes/treatment with drugs 

├── LICENSE
├── Makefile           <- Makefile with commands like `make data` or `make train`
├── README.md          <- The top-level README for developers using this project.
├── data               <- Input data files used for the project 
│
├── docs               <- Contains documents such as presentation slides pertaining to project
│
├── references         <- References to the algorithms employed
│
├── reports            <- Generated analysis as HTML, PDF, LaTeX, etc. -- currently empty
│   └── figures        <- Generated graphics and figures to be used in reporting -- currently empty
│
├── requirements.txt   <- The requirements file for reproducing the analysis environment, e.g.
│                         generated with `pip freeze > requirements.txt`
│
├── setup.py           <- makes project pip installable (pip install -e .) so src can be imported
├── src                <- Source code for use in this project.
│   ├── __init__.py    <- Makes src a Python module
│   │
│   ├── data           <- Scripts to download or generate data -- currently unmodified
│   │   └── make_dataset.py
│   │
│   ├── features       <- Scripts to turn raw data into features for modeling
│   │   └── build_features.py
│   │
│   ├── models         <- Scripts to train models and then use trained models to make
│   │   │                 predictions -- currently empty
│   │   ├── predict_model.py
│   │   └── train_model.py
│   │
│   └── visualization  <- Scripts to create exploratory and results oriented visualizations
│       └── visualize.py
│
└── tox.ini            <- tox file with settings for running tox; see tox.testrun.org