jupyter widget bindings for the motif library
Project description
Pymotif
A Python package that lets you plot Motif graphs within Jupyter Notebook / Jupyter Lab:
It's that easy to get started!
Features
- Seamless integration into existing Jupyter workflows
- Multiple data import options
- Programmatic graph manipulation
- Easy code sharing and reuse
Installation
You can install using pip
(we recommend using virtual environments):
pip install pymotif
And it should work. In some cases, you may also need to install and enable Jupyter extensions:
# Jupyter Lab
jupyter labextension install @jupyter-widgets/jupyterlab-manager
# For Jupyter Lab <= 2, you may need to install the extension manually
jupyter labextension install @cylynx/pymotif
# For Jupyter Notebook <= 5.2, you may need to enable nbextensions
jupyter nbextension enable --py [--sys-prefix|--user|--system] pymotif
Demo
Demo notebooks can be found in the examples
folder. For a start, check out examples/introduction.ipynb
, which gives a quick overview of the available functionality!
Motif Class
As shown above, using Motif in Jupyter involves importing and instantiating the Motif
class from pymotif
.
Instantiation
from pymotif import Motif
motif = Motif()
motif.plot() # or just 'motif'
Motif()
accepts various instantiation parameters (refer to Motif's __init__
method for updated information):
All parameters are optional.
Only one graph import (json_path, nx_graph, neo4j_graph, or csv_path) can be passed each time.
json_path: str
Path to a local JSON file containing the graph data.
If this is used, all other params will be ignored.
nx_graph: nx.Graph
A networkx graph to be rendered
neo4j_graph: neo4j.graph.Graph
A neo4j graph to be rendered, obtained from the neo4j.Result.graph() method.
Ref: https://neo4j.com/docs/api/python-driver/current/api.html#graph
csv_path: str
Path to a local CSV edgelist file
style: dict
The rendered graph's style. Its format depends on Motif's StyleOptions interface:
https://github.com/cylynx/motif.gl/blob/c79ba6549407979a4ec0214cc6c7c7d0f2a3be41/packages/motif/src/redux/graph/types.ts#L206
title: str
The rendered graph's title
Other params are ignored when using JSON files because the file itself may also contain pre-defined styles, titles, or other settings.
Example Usage
# import a csv file and set a title
motif = Motif(csv_path=<YOUR CSV PATH>, title='my first csv import')
# import a json file. as mentioned above, using json ignores all other params
motif = Motif(json_path=<YOUR JSON PATH>, title='ignored parameter')
# import a networkx graph and arrange it in a grid layout
style = {'layout': {'type': 'grid'}}
motif = Motif(nx_graph=<YOUR NETWORKX GRAPH>, style=style)
Attributes
There is only one class attribute for now:
state: dict
There are 2 possible keys: data, style.
Data is a list of graph data describing what will be rendered in the widget.
Style is a dict describing how the graphs will be rendered.
Follows the TLoadFormat interface defined in Motif's types.ts:
https://github.com/cylynx/motif.gl/blob/master/packages/motif/src/redux/graph/types.ts#L283
Example Usage
m = Motif(<YOUR PARAMS>)
# check graph's initial state
m.state
# stuff happens
...
# sanity check
m.state
This may be useful for debugging your graph objects at various points in time throughout your analysis.
Methods
def add_graph(self, **kwargs):
"""
Adds another graph to an existing Motif widget.
Takes the same parameters as __init__.
If provided, graph settings here will overwrite those set previously (e.g. style).
"""
def set_style(self, style: dict, overwrite=False):
"""
Allows updating the style of an existing widget.
------------
Parameters
------------
style: dict
The rendered graph's style
overwrite=False:
If True, overwrites all existing styles with the passed 'style' param.
If False, merges 'style' param with existing styles
"""
def plot(self):
""" Plots the graphs' current state as a Jupyter widget """
Example Usage
# create a new graph
m = Motif(<YOUR PARAMS>)
# add another previously-saved graph from a JSON file
m.add_graph(json_path=<YOUR JSON PATH>)
# adjust and overwrite the combined graphs' style
m.set_style(style=<YOUR STYLE>, overwrite=True)
# plot the combined graph
m.plot()
Development
This section contains instructions for developing Pymotif locally.
For a more thorough walkthrough check out the official Jupyter widgets guide:
https://ipywidgets.readthedocs.io/en/latest/examples/Widget%20Custom.html
Create a new conda environment with the dependencies
To create the environment, execute the following command:
conda create -n motif -c conda-forge jupyterlab nodejs python
Then activate the environment with:
conda activate motif
Build and install the widget for development
Since the widget contains a Python part, you need to install the package in editable mode:
npm run pymotif:build // In root directory to link it with monorepo setup
python -m pip install -e .
If you are using JupyterLab:
jupyter labextension develop --overwrite .
If you are using the Classic Notebook:
jupyter nbextension install --sys-prefix --symlink --overwrite --py pymotif
jupyter nbextension enable --sys-prefix --py pymotif
To continuously monitor the project for changes and automatically trigger a rebuild, start Jupyter in watch mode:
jupyter lab --watch
And in a separate session, begin watching the source directory for changes:
npm run pymotif // In root directory to link it with monorepo setup
After a change wait for the build to finish and then refresh your browser and the changes should take effect.
If you make a change to the python code then you will need to restart the notebook kernel to have it take effect.
Publishing
- Update the version in package.json
- Relase the
@cylynx/pymotif
packages:
npm login
npm run pymotif:publish
- Bundle the python package:
python setup.py sdist bdist_wheel
- Update the version in
pymotif/_version.py
- If frontend version dependency has changed, update
pymotif/_frontend.py
- Publish the package to PyPI:
pip install twine
twine upload dist/pymotif*
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