Show Sidebar Hide Sidebar

Spectral Biclustering algorithm in Scikit-learn

This example demonstrates how to generate a checkerboard dataset and bicluster it using the Spectral Biclustering algorithm.

The data is generated with the make_checkerboard function, then shuffled and passed to the Spectral Biclustering algorithm. The rows and columns of the shuffled matrix are rearranged to show the biclusters found by the algorithm. The outer product of the row and column label vectors shows a representation of the checkerboard structure.

New to Plotly?

Plotly's Python library is free and open source! Get started by downloading the client and reading the primer.
You can set up Plotly to work in online or offline mode, or in jupyter notebooks.
We also have a quick-reference cheatsheet (new!) to help you get started!

Version

In [1]:
import sklearn
sklearn.__version__
Out[1]:
'0.18'

Imports

This Tutorial imports make_checkerboard and consensus_score

In [2]:
print(__doc__)

import plotly.plotly as py
from plotly import tools
import plotly.graph_objs as go

import numpy as np
from matplotlib import pyplot as plt

from sklearn.datasets import make_checkerboard
from sklearn.datasets import samples_generator as sg
from sklearn.cluster.bicluster import SpectralBiclustering
from sklearn.metrics import consensus_score
Automatically created module for IPython interactive environment

Calculations and Plots

In [3]:
def matplotlib_to_plotly(cmap, pl_entries):
    h = 1.0/(pl_entries-1)
    pl_colorscale = []
    
    for k in range(pl_entries):
        C = map(np.uint8, np.array(cmap(k*h)[:3])*255)
        pl_colorscale.append([k*h, 'rgb'+str((C[0], C[1], C[2]))])
        
    return pl_colorscale

n_clusters = (4, 3)
data, rows, columns = make_checkerboard(
    shape=(300, 300), n_clusters=n_clusters, noise=10,
    shuffle=False, random_state=0)

original_dataset = go.Heatmap(z=data, colorscale=
                              matplotlib_to_plotly(plt.cm.Blues,len(data)),
                              showscale=False)

data, row_idx, col_idx = sg._shuffle(data, random_state=0)

shuffled_dataset = go.Heatmap(z=data, colorscale=
                              matplotlib_to_plotly(plt.cm.Blues,len(data)),
                              showscale=False)

model = SpectralBiclustering(n_clusters=n_clusters, method='log',
                             random_state=0)
model.fit(data)
score = consensus_score(model.biclusters_,
                        (rows[:, row_idx], columns[:, col_idx]))

print("consensus score: {:.1f}".format(score))

fit_data = data[np.argsort(model.row_labels_)]
fit_data = fit_data[:, np.argsort(model.column_labels_)]

after_biclustering = go.Heatmap(z=fit_data, colorscale=
                               matplotlib_to_plotly(plt.cm.Blues,len(data)),
                               showscale=False)

checkerboard_structure = go.Heatmap(z=np.outer(np.sort(model.row_labels_) + 1,
                                              np.sort(model.column_labels_) + 1),
                                  colorscale=
                                  matplotlib_to_plotly(plt.cm.Blues,len(data)),
                                  showscale=False)
consensus score: 1.0
In [4]:
fig = tools.make_subplots(rows=2, cols=2,
                          subplot_titles=('Original dataset','Shuffled dataset', 
                                          'After biclustering: rearranged to show biclusters',
                                          'Checkerboard structure of rearranged data'))
fig.append_trace(original_dataset, 1, 1)
fig.append_trace(shuffled_dataset, 1, 2)
fig.append_trace(after_biclustering, 2, 1)
fig.append_trace(checkerboard_structure, 2, 2)

fig['layout'].update(height=900)
py.iplot(fig)
This is the format of your plot grid:
[ (1,1) x1,y1 ]  [ (1,2) x2,y2 ]
[ (2,1) x3,y3 ]  [ (2,2) x4,y4 ]

Out[4]:

License

Author:

    Kemal Eren <kemal@kemaleren.com>

License:

     BSD 3 clause
Still need help?
Contact Us

For guaranteed 24 hour response turnarounds, upgrade to a Developer Support Plan.