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<p class="first admonition-title">Note</p>
<p class="last">Click <a class="reference internal" href="#sphx-glr-download-auto-examples-bicluster-plot-spectral-biclustering-py"><span class="std std-ref">here</span></a> to download the full example code</p>
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<div class="sphx-glr-example-title section" id="a-demo-of-the-spectral-biclustering-algorithm">
<span id="sphx-glr-auto-examples-bicluster-plot-spectral-biclustering-py"></span><h1>A demo of the Spectral Biclustering algorithm<a class="headerlink" href="#a-demo-of-the-spectral-biclustering-algorithm" title="Permalink to this headline">¶</a></h1>
<p>This example demonstrates how to generate a checkerboard dataset and
bicluster it using the Spectral Biclustering algorithm.</p>
<p>The data is generated with the <code class="docutils literal"><span class="pre">make_checkerboard</span></code> 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.</p>
<p>The outer product of the row and column label vectors shows a
representation of the checkerboard structure.</p>
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<li><img alt="../../_images/sphx_glr_plot_spectral_biclustering_001.png" class="sphx-glr-multi-img first" src="../../_images/sphx_glr_plot_spectral_biclustering_001.png" />
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<li><img alt="../../_images/sphx_glr_plot_spectral_biclustering_002.png" class="sphx-glr-multi-img first" src="../../_images/sphx_glr_plot_spectral_biclustering_002.png" />
</li>
<li><img alt="../../_images/sphx_glr_plot_spectral_biclustering_003.png" class="sphx-glr-multi-img first" src="../../_images/sphx_glr_plot_spectral_biclustering_003.png" />
</li>
<li><img alt="../../_images/sphx_glr_plot_spectral_biclustering_004.png" class="sphx-glr-multi-img first" src="../../_images/sphx_glr_plot_spectral_biclustering_004.png" />
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<p class="sphx-glr-script-out">Out:</p>
<div class="sphx-glr-script-out highlight-none"><div class="highlight"><pre><span></span>consensus score: 1.0
</pre></div>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">print</span><span class="p">(</span><span class="vm">__doc__</span><span class="p">)</span>
<span class="c1"># Author: Kemal Eren <[email protected]></span>
<span class="c1"># License: BSD 3 clause</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">matplotlib</span> <span class="k">import</span> <span class="n">pyplot</span> <span class="k">as</span> <span class="n">plt</span>
<span class="kn">from</span> <span class="nn">sklearn.datasets</span> <span class="k">import</span> <a href="../../modules/generated/sklearn.datasets.make_checkerboard.html#sklearn.datasets.make_checkerboard" title="View documentation for sklearn.datasets.make_checkerboard"><span class="n">make_checkerboard</span></a>
<span class="kn">from</span> <span class="nn">sklearn.datasets</span> <span class="k">import</span> <span class="n">samples_generator</span> <span class="k">as</span> <span class="n">sg</span>
<span class="kn">from</span> <span class="nn">sklearn.cluster.bicluster</span> <span class="k">import</span> <span class="n">SpectralBiclustering</span>
<span class="kn">from</span> <span class="nn">sklearn.metrics</span> <span class="k">import</span> <a href="../../modules/generated/sklearn.metrics.consensus_score.html#sklearn.metrics.consensus_score" title="View documentation for sklearn.metrics.consensus_score"><span class="n">consensus_score</span></a>
<span class="n">n_clusters</span> <span class="o">=</span> <span class="p">(</span><span class="mi">4</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
<span class="n">data</span><span class="p">,</span> <span class="n">rows</span><span class="p">,</span> <span class="n">columns</span> <span class="o">=</span> <a href="../../modules/generated/sklearn.datasets.make_checkerboard.html#sklearn.datasets.make_checkerboard" title="View documentation for sklearn.datasets.make_checkerboard"><span class="n">make_checkerboard</span></a><span class="p">(</span>
<span class="n">shape</span><span class="o">=</span><span class="p">(</span><span class="mi">300</span><span class="p">,</span> <span class="mi">300</span><span class="p">),</span> <span class="n">n_clusters</span><span class="o">=</span><span class="n">n_clusters</span><span class="p">,</span> <span class="n">noise</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span>
<span class="n">shuffle</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<a href="https://matplotlib.org/api/_as_gen/matplotlib.pyplot.matshow.html#matplotlib.pyplot.matshow" title="View documentation for matplotlib.pyplot.matshow"><span class="n">plt</span><span class="o">.</span><span class="n">matshow</span></a><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">cmap</span><span class="o">=</span><span class="n">plt</span><span class="o">.</span><span class="n">cm</span><span class="o">.</span><span class="n">Blues</span><span class="p">)</span>
<a href="https://matplotlib.org/api/_as_gen/matplotlib.pyplot.title.html#matplotlib.pyplot.title" title="View documentation for matplotlib.pyplot.title"><span class="n">plt</span><span class="o">.</span><span class="n">title</span></a><span class="p">(</span><span class="s2">"Original dataset"</span><span class="p">)</span>
<span class="n">data</span><span class="p">,</span> <span class="n">row_idx</span><span class="p">,</span> <span class="n">col_idx</span> <span class="o">=</span> <span class="n">sg</span><span class="o">.</span><span class="n">_shuffle</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<a href="https://matplotlib.org/api/_as_gen/matplotlib.pyplot.matshow.html#matplotlib.pyplot.matshow" title="View documentation for matplotlib.pyplot.matshow"><span class="n">plt</span><span class="o">.</span><span class="n">matshow</span></a><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">cmap</span><span class="o">=</span><span class="n">plt</span><span class="o">.</span><span class="n">cm</span><span class="o">.</span><span class="n">Blues</span><span class="p">)</span>
<a href="https://matplotlib.org/api/_as_gen/matplotlib.pyplot.title.html#matplotlib.pyplot.title" title="View documentation for matplotlib.pyplot.title"><span class="n">plt</span><span class="o">.</span><span class="n">title</span></a><span class="p">(</span><span class="s2">"Shuffled dataset"</span><span class="p">)</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">SpectralBiclustering</span><span class="p">(</span><span class="n">n_clusters</span><span class="o">=</span><span class="n">n_clusters</span><span class="p">,</span> <span class="n">method</span><span class="o">=</span><span class="s1">'log'</span><span class="p">,</span>
<span class="n">random_state</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">model</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="n">score</span> <span class="o">=</span> <a href="../../modules/generated/sklearn.metrics.consensus_score.html#sklearn.metrics.consensus_score" title="View documentation for sklearn.metrics.consensus_score"><span class="n">consensus_score</span></a><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">biclusters_</span><span class="p">,</span>
<span class="p">(</span><span class="n">rows</span><span class="p">[:,</span> <span class="n">row_idx</span><span class="p">],</span> <span class="n">columns</span><span class="p">[:,</span> <span class="n">col_idx</span><span class="p">]))</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"consensus score: </span><span class="si">{:.1f}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">score</span><span class="p">))</span>
<span class="n">fit_data</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><a href="https://docs.scipy.org/doc/numpy/reference/generated/numpy.argsort.html#numpy.argsort" title="View documentation for numpy.argsort"><span class="n">np</span><span class="o">.</span><span class="n">argsort</span></a><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">row_labels_</span><span class="p">)]</span>
<span class="n">fit_data</span> <span class="o">=</span> <span class="n">fit_data</span><span class="p">[:,</span> <a href="https://docs.scipy.org/doc/numpy/reference/generated/numpy.argsort.html#numpy.argsort" title="View documentation for numpy.argsort"><span class="n">np</span><span class="o">.</span><span class="n">argsort</span></a><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">column_labels_</span><span class="p">)]</span>
<a href="https://matplotlib.org/api/_as_gen/matplotlib.pyplot.matshow.html#matplotlib.pyplot.matshow" title="View documentation for matplotlib.pyplot.matshow"><span class="n">plt</span><span class="o">.</span><span class="n">matshow</span></a><span class="p">(</span><span class="n">fit_data</span><span class="p">,</span> <span class="n">cmap</span><span class="o">=</span><span class="n">plt</span><span class="o">.</span><span class="n">cm</span><span class="o">.</span><span class="n">Blues</span><span class="p">)</span>
<a href="https://matplotlib.org/api/_as_gen/matplotlib.pyplot.title.html#matplotlib.pyplot.title" title="View documentation for matplotlib.pyplot.title"><span class="n">plt</span><span class="o">.</span><span class="n">title</span></a><span class="p">(</span><span class="s2">"After biclustering; rearranged to show biclusters"</span><span class="p">)</span>
<a href="https://matplotlib.org/api/_as_gen/matplotlib.pyplot.matshow.html#matplotlib.pyplot.matshow" title="View documentation for matplotlib.pyplot.matshow"><span class="n">plt</span><span class="o">.</span><span class="n">matshow</span></a><span class="p">(</span><a href="https://docs.scipy.org/doc/numpy/reference/generated/numpy.outer.html#numpy.outer" title="View documentation for numpy.outer"><span class="n">np</span><span class="o">.</span><span class="n">outer</span></a><span class="p">(</span><a href="https://docs.scipy.org/doc/numpy/reference/generated/numpy.sort.html#numpy.sort" title="View documentation for numpy.sort"><span class="n">np</span><span class="o">.</span><span class="n">sort</span></a><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">row_labels_</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span>
<a href="https://docs.scipy.org/doc/numpy/reference/generated/numpy.sort.html#numpy.sort" title="View documentation for numpy.sort"><span class="n">np</span><span class="o">.</span><span class="n">sort</span></a><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">column_labels_</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">),</span>
<span class="n">cmap</span><span class="o">=</span><span class="n">plt</span><span class="o">.</span><span class="n">cm</span><span class="o">.</span><span class="n">Blues</span><span class="p">)</span>
<a href="https://matplotlib.org/api/_as_gen/matplotlib.pyplot.title.html#matplotlib.pyplot.title" title="View documentation for matplotlib.pyplot.title"><span class="n">plt</span><span class="o">.</span><span class="n">title</span></a><span class="p">(</span><span class="s2">"Checkerboard structure of rearranged data"</span><span class="p">)</span>
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