Bio-Roary
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<div class=" highlight hl-ipython2"><pre><span class="c"># Plot the pangenome pie chart</span>
<span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="mi">1...
<span class="n">core</span> <span class="o">=</span> <span class="n">roary</span><span class="p">[</span><span class="n">roary</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">...
<span class="n">softcore</span> <span class="o">=</span> <span class="n">roary</span><span class="p">[(</span><span class="n">roary</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class...
<span class="p">(</span><span class="n">roary</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> <span ...
<span class="n">shell</span> <span class="o">=</span> <span class="n">roary</span><span class="p">[(</span><span class="n">roary</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o...
<span class="p">(</span><span class="n">roary</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> <span ...
<span class="n">cloud</span> <span class="o">=</span> <span class="n">roary</span><span class="p">[</span><span class="n">roary</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o"...
<span class="n">total</span> <span class="o">=</span> <span class="n">roary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">my_autopct</span><span class="p">(</span><span class="n">pct</span><span class="p">):</span>
<span class="n">val</span><span class="o">=</span><span class="nb">int</span><span class="p">(</span><span class="n">pct</span><span class="o">*</span><span class="n">total</span><span class="o">/</span><span class="mf">100.0</span><span class="p...
<span class="k">return</span> <span class="s">'{v:d}'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">v</span><span class="o">=</span><span class="n">val</span><span class="p">)</span>
<span class="n">a</span><span class="o">=</span><span class="n">plt</span><span class="o">.</span><span class="n">pie</span><span class="p">([</span><span class="n">core</span><span class="p">,</span> <span class="n">softcore</span><span class="p">,<...
<span class="n">labels</span><span class="o">=</span><span class="p">[</span><span class="s">'core</span><span class="se">\n</span><span class="s">(</span><span class="si">%d</span><span class="s"> strains)'</span><span class="o">%</span><span ...
<span class="s">'soft-core</span><span class="se">\n</span><span class="s">(</span><span class="si">%d</span><span class="s"> <= strains < </span><span class="si">%d</span><span class="s">)'</span><span class="o">%</span><span cla...
<span class="n">roary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span>
<span class="s">'shell</span><span class="se">\n</span><span class="s">(</span><span class="si">%d</span><span class="s"> <= strains < </span><span class="si">%d</span><span class="s">)'</span><span class="o">%</span><span class="...
<span class="n">roary</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*.</span><span class="mi">95</span><...
<span class="s">'cloud</span><span class="se">\n</span><span class="s">(strains < </span><span class="si">%d</span><span class="s">)'</span><span class="o">%</span><span class="p">(</span><span class="n">roary</span><span class="o">....
<span class="n">explode</span><span class="o">=</span><span class="p">[</span><span class="mf">0.1</span><span class="p">,</span> <span class="mf">0.05</span><span class="p">,</span> <span class="mf">0.02</span><span class="p">,</span> <span cl...
<span class="n">colors</span><span class="o">=</span><span class="p">[(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="nb"...
<span class="n">autopct</span><span class="o">=</span><span class="n">my_autopct</span><span class="p">)</span>
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