Clustergrammer-Widget

This is a Jupyter notebook interactive widget implementation of the interactive heatmap tool Clustergrammer. The front-end visualization, clustergrammer.js is built using D3.js and the back-end, clustergrammer.py is built in Python.

Please refer to the Clustergrammer-Widget documentation for more information or click on the screenshot below to see an example notebook.

Installation

The interactive widget can be installed and enabled using the following commands:

pip install clustergrammer_widget
jupyter nbextension enable --py --sys-prefix widgetsnbextension
jupyter nbextension enable --py --sys-prefix clustergrammer_widget

Dependencies

• Numpy
• Scipy
• Pandas

Clustergrammer-widget is compatable with Python 2 and 3.

Example Workflow

The Clustergrammer-widget can be used to visualize a matrix of your data in the TSV format described here.

Within the Jupyter/IPython notebook the widget can be run using the following commands

# import the widget
from clustergrammer_widget import *

# load data into new network instance and cluster
net = Network(clustergrammer_widget)
net.load_file('rc_two_cats.txt')
net.cluster()

# view the results as a widget
net.widget()

Case Studies and Examples

The Clustergrammer-Widget has been applied to a wide variety of biological and non-biological data. Refer to the Jupyter notebook examples below and Case Studies and Examples for more information:

• Running Clustergrammer Widget
• DataFrame Example
• CCLE Jupyter Notebook
• Lung Cancer PTM and Gene Expression Regulation
• Single-Cell CyTOF Data
• MNIST Notebook
• USDA Nutrient Dataset
• Iris Dataset

Development Installation

For a development installation (requires npm),

$ git clone https://github.com/maayanlab/clustergrammer-widget.git
$ cd clustergrammer-widget
$ pip install -e .
$ jupyter nbextension install --py --symlink --user clustergrammer_widget
$ jupyter nbextension enable --py --user clustergrammer_widget