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
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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