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Embark on a journey of single-cell data exploration.

Project description

|Build Status|\ |Coverage Status|

flotilla
========

.. figure:: flotilla.png
:alt: flotilla Logo

flotilla Logo
Installation instructions
=========================

From a clean install of Mavericks 10.9.4, follow these steps.

All others must fend for themselves to install matplotlib, scipy and
their third-party dependencies.

*This part only needs to be done once*

- `Install anaconda <https://store.continuum.io/cshop/anaconda/>`__
- `Install Xcode (this can take an
hour) <https://itunes.apple.com/us/app/xcode/id497799835?mt=12>`__
- Open Xcode and agree to terms and services (it is very important to
read them thoroughly)
- Install `homebrew <http://brew.sh/>`__

``ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"``

- Install freetype:

``brew install freetype``

- Install heavy packages (this can take an hour or more)

::

conda install pip numpy scipy cython matplotlib nose six scikit-learn ipython networkx pandas tornado statsmodels setuptools pytest pyzmq jinja2 pyyaml`

- Create a virtual environment
``conda create -n flotilla_env pip numpy scipy cython matplotlib nose six scikit-learn ipython networkx pandas tornado statsmodels setuptools pytest pyzmq jinja2 pyyaml```

- Switch to virtual environment

``source activate flotilla_env``

- Install flotilla and its dependencies (this can take a few minutes):

``pip install git+https://github.com/YeoLab/flotilla.git``

- Create a scratch space for your work

``mkdir ~/flotilla_scratch``

- Make a place to store flotilla projects

``mkdir ~/flotilla_projects``

- Go back to the real world

``source deactivate``

Start using flotilla:
=====================

Use the above instructions to create a flotilla-friendly environment,
then:

- switch to virtual environment

``source activate flotilla_env``

- start an ipython notebook:

``ipython notebook --notebook-dir=~/flotilla_scratch``

- create a new notebook by clicking ``New Notebook``
- rename your notebook from "Untitled" to something more informative by
clicking the title panel.
- load matplotlib backend using every notebook must use this to display
inline output

``%matplotlib inline``

Test interactive features with example data:
--------------------------------------------

We have prepared a slice of the full dataset for testing and
demonstration purposes.

Run each of the following code lines in its own ipython notebook cell
for an interactive feature.

::

import flotilla
test_study = flotilla.embark('http://sauron.ucsd.edu/flotilla_projects/neural_diff_chr22/datapackage.json')

test_study.interactive_pca()

test_study.interactive_graph()

test_study.interactive_classifier()

test_study.interactive_lavalamp_pooled_inconsistent()

IMPORTANT NOTE: for this test,several failures are expected since the
test set is small. Adjust parameters to explore valid parameter spaces.
For example, you can manually select ``all_genes`` as the
``feature_subset`` from the drop-down menu that appears after running
these interactive functions.

.. |Build Status| image:: https://travis-ci.org/YeoLab/flotilla.svg?branch=master
:target: https://travis-ci.org/YeoLab/flotilla
.. |Coverage Status| image:: https://img.shields.io/coveralls/YeoLab/flotilla.svg
:target: https://coveralls.io/r/YeoLab/flotilla?branch=master

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