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<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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        <a href="core-module.html">Package&nbsp;core</a> ::
        Module&nbsp;PlotData
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<h1 class="epydoc">Source Code for <a href="core.PlotData-module.html">Module core.PlotData</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-docstring">'''
</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-docstring">Created  2012
</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-docstring">@author: GieseS
</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-docstring">Little plotting script which is called in the analysis of different mappings to an artificial reference genome.
</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-docstring">It produces the following plots:
</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-docstring">1) ROC Curve
</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-docstring">2) Overview histograms for FP / TP.
</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-docstring">
</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-docstring">'''</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line">
 </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">as</tt> <tt class="py-name">np</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">matplotlib</tt><tt class="py-op">.</tt><tt class="py-name">pyplot</tt> <tt class="py-keyword">as</tt> <tt class="py-name">plt</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">mpl_toolkits</tt><tt class="py-op">.</tt><tt class="py-name">mplot3d</tt> <tt class="py-keyword">import</tt> <tt class="py-name">Axes3D</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">random</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">time</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">pylab</tt> <tt class="py-keyword">as</tt> <tt class="py-name">p</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">
 </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-comment">##### HELP FUNCTIONS ####</tt>
 </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line">
 </tt>
<a name="trapezoidal_rule"></a><div id="trapezoidal_rule-def"><a name="L27"></a><tt class="py-lineno"> 27</tt> <a class="py-toggle" href="#" id="trapezoidal_rule-toggle" onclick="return toggle('trapezoidal_rule');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.PlotData-module.html#trapezoidal_rule">trapezoidal_rule</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt> <tt class="py-param">y</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="trapezoidal_rule-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="trapezoidal_rule-expanded"><a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">    <tt class="py-docstring">"""Approximates the integral through the points a,b"""</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">    <tt class="py-name">index</tt> <tt class="py-op">=</tt>  <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">    <tt class="py-name">xdiff</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">    <tt class="py-name">ysum</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">y</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-name">y</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">dot</tt><tt class="py-op">(</tt><tt class="py-name">xdiff</tt><tt class="py-op">,</tt><tt class="py-name">ysum</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
</div><a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">
 </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">
 </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt class="py-comment">#### HELP FUNCTIONS END ############</tt>
 </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">
 </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">
 </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"><tt class="py-string">""" 
</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"><tt class="py-string">abbreviations:
</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"><tt class="py-string">tp = True positives
</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line"><tt class="py-string">fp = false positives
</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"><tt class="py-string">NM = number of mismtaches
</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt class="py-string">mq = mapping quality
</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"><tt class="py-string">rq = readquality
</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-string">subs = substitutions in artifical reference genome (ARG)
</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">
 </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">
 </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">            
 </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"><tt class="py-comment">###############################################################################            </tt>
 </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">
 </tt>
<a name="CalculateRoc2"></a><div id="CalculateRoc2-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="CalculateRoc2-toggle" onclick="return toggle('CalculateRoc2');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.PlotData-module.html#CalculateRoc2">CalculateRoc2</a><tt class="py-op">(</tt><tt class="py-param">dataArray</tt><tt class="py-op">,</tt><tt class="py-param">prefix</tt><tt class="py-op">,</tt><tt class="py-param">readsize</tt><tt class="py-op">,</tt><tt class="py-param">uniquehits</tt><tt class="py-op">,</tt><tt class="py-param">mappedreads</tt><tt class="py-op">,</tt><tt class="py-param">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CalculateRoc2-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CalculateRoc2-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">    <tt class="py-docstring">"""
</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"><tt class="py-docstring">    Calculates the adjusted ROC curve as well as the AUC value derived from the adjusted points
</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"><tt class="py-docstring">    and writes the ROC tables to .txt files. 
</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">    <tt class="py-name">starttime</tt><tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">    <tt class="py-name">uniquehits</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">uniquehits</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">    <tt class="py-name">readsize</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">readsize</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">    
 </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">    
 </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">    <tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">        
 </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">
 </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">    <tt class="py-name">resultmatrix</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">entries</tt><tt class="py-op">*</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">    <tt class="py-name">resultmatrix</tt> <tt class="py-op">=</tt> <tt class="py-name">resultmatrix</tt><tt class="py-op">.</tt><tt class="py-name">reshape</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">entries</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">        
 </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">    <tt class="py-name">maxrq</tt> <tt class="py-op">=</tt>  <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">rq</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">    <tt class="py-name">maxnm</tt> <tt class="py-op">=</tt>  <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">    <tt class="py-name">maxGaps</tt><tt class="py-op">=</tt>  <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">    <tt class="py-name">maxMism</tt><tt class="py-op">=</tt>  <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">    
 </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">        
 </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">    <tt class="py-name">minrq</tt> <tt class="py-op">=</tt>  <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">rq</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">    <tt class="py-name">minnm</tt> <tt class="py-op">=</tt>  <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">nm</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">    <tt class="py-name">minmq</tt><tt class="py-op">=</tt>  <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">mq</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">    <tt class="py-name">minGaps</tt><tt class="py-op">=</tt>  <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt>   </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">    <tt class="py-name">minMism</tt><tt class="py-op">=</tt>  <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt><tt class="py-op">)</tt>       </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">    
 </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">    
 </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">    <tt class="py-comment"># adjust stepsize for rq since the score behaves the other way</tt>
 </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">    <tt class="py-name">quants</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">,</tt><tt class="py-number">4</tt><tt class="py-op">,</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">    <tt class="py-name">tempa</tt> <tt class="py-op">=</tt> <tt class="py-name">maxrq</tt><tt class="py-op">-</tt><tt class="py-name">minrq</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">    <tt class="py-name">stepsize</tt> <tt class="py-op">=</tt> <tt class="py-name">tempa</tt><tt class="py-op">/</tt><tt class="py-number">5</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">        
 </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">    <tt class="py-name">rqQuants</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">round</tt><tt class="py-op">(</tt><tt class="py-name">minrq</tt><tt class="py-op">+</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">stepsize</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quants</tt><tt class="py-op">]</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">    <tt class="py-name">rqQuants</tt><tt class="py-op">.</tt><tt class="py-name">reverse</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">    <tt class="py-name">rqQuants</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt><tt class="py-number">0</tt> <tt class="py-comment"># last entry is rounded bigger than the smallest in the dataset</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">        
 </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">    <tt class="py-name">nmQuants</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">*</tt><tt class="py-name">maxnm</tt><tt class="py-op">/</tt><tt class="py-number">5</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quants</tt><tt class="py-op">]</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">    <tt class="py-name">GapsQuants</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">*</tt><tt class="py-name">maxGaps</tt><tt class="py-op">/</tt><tt class="py-number">5</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quants</tt><tt class="py-op">]</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">    <tt class="py-name">MismQuants</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">*</tt><tt class="py-name">maxMism</tt><tt class="py-op">/</tt><tt class="py-number">5</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quants</tt><tt class="py-op">]</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">
 </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">    <tt class="py-name">rocvector</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">        
 </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">    <tt class="py-comment"># i = NM,l = RQ, k = MQ</tt>
 </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quants</tt><tt class="py-op">:</tt> <tt class="py-comment"># RQ</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quants</tt><tt class="py-op">:</tt> <tt class="py-comment"># GAPS</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">                    <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quants</tt><tt class="py-op">:</tt> <tt class="py-comment"># MISMATCH</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">                            <tt class="py-name">temparray</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">m</tt> <tt class="py-keyword">for</tt> <tt class="py-name">m</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataArray</tt> <tt class="py-keyword">if</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt class="py-name">gaps</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">GapsQuants</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt class="py-name">mism</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">MismQuants</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt>  <tt class="py-keyword">and</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt class="py-name">rq</tt> <tt class="py-op">&gt;=</tt><tt class="py-name">rqQuants</tt><tt class="py-op">[</tt><tt class="py-name">l</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">                            
 </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">
 </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">                            <tt class="py-name">tempids</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt class="py-name">id</tt> <tt class="py-keyword">for</tt> <tt class="py-name">m</tt> <tt class="py-keyword">in</tt> <tt class="py-name">temparray</tt><tt class="py-op">]</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">                            <tt class="py-name">uniquereads</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">                            <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">tempids</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">                                <tt class="py-name">uniquereads</tt><tt class="py-op">[</tt><tt class="py-name">tempids</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">
 </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">                            <tt class="py-name">mappedreads</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">uniquereads</tt><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">                            
 </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line"> 
 </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">                            
 </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">                            <tt class="py-name">templength</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">temparray</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">                            
 </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">                            <tt class="py-keyword">if</tt> <tt class="py-name">templength</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">                                <tt class="py-keyword">continue</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">                            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">                                <tt class="py-name">tempTP</tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">mr</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">temparray</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">                                <tt class="py-name">tempFP</tt> <tt class="py-op">=</tt><tt class="py-name">templength</tt><tt class="py-op">-</tt><tt class="py-name">tempTP</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">                                <tt class="py-name">F</tt> <tt class="py-op">=</tt> <tt class="py-name">round</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">mappedreads</tt><tt class="py-op">)</tt><tt class="py-op">/</tt> <tt class="py-name">readsize</tt><tt class="py-op">)</tt> <tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">                                <tt class="py-name">sens</tt> <tt class="py-op">=</tt> <tt class="py-name">round</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">tempTP</tt><tt class="py-op">/</tt> <tt class="py-name">uniquehits</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">F</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">                                <tt class="py-keyword">if</tt> <tt class="py-name">tempFP</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">                                    <tt class="py-name">spec</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">                                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">                                    <tt class="py-name">spec</tt> <tt class="py-op">=</tt> <tt class="py-name">round</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">tempFP</tt> <tt class="py-op">/</tt> <tt class="py-name">uniquehits</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">F</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt>                     </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">                                
 </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">                                <tt class="py-name">rocvector</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">rqQuants</tt><tt class="py-op">[</tt><tt class="py-name">l</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">GapsQuants</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">MismQuants</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">tempTP</tt><tt class="py-op">,</tt><tt class="py-name">tempFP</tt><tt class="py-op">,</tt><tt class="py-name">templength</tt><tt class="py-op">,</tt><tt class="py-name">sens</tt><tt class="py-op">,</tt><tt class="py-name">spec</tt><tt class="py-op">,</tt><tt class="py-name">F</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">                        
 </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">                    <tt class="py-comment">#print ("%d\t%d\t%d\t" % (templength,tempTP,tempFP))</tt>
 </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">
 </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">    <tt class="py-comment">#0 = NM        4 = TP        7 = sens</tt>
 </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">    <tt class="py-comment">#1 = RQ        5 = FP        8 = 1-spec</tt>
 </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">    <tt class="py-comment">#2 = GAPS        6 = P        9 = F</tt>
 </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">    <tt class="py-comment">#append needed for last entry in AUC calculation</tt>
 </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">    <tt class="py-name">rocvector</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt>                 </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">    <tt class="py-name">nproc</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">rocvector</tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">    
 </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">    <tt class="py-comment">#write the sens and specificity values from nproc according to the enumeration in line 149. </tt>
 </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">    <tt class="py-comment">#specificity is in cell -2</tt>
 </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">    <tt class="py-comment"># sensitivity is in cell -3</tt>
 </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">    <tt class="py-name">sens</tt> <tt class="py-op">=</tt>  <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">nproc</tt><tt class="py-op">]</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">    <tt class="py-name">spez</tt> <tt class="py-op">=</tt>  <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">nproc</tt><tt class="py-op">]</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">    
 </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">    <tt class="py-comment"># adjust ROC curve. It is necessary that it the 1-specificity ends in 1.</tt>
 </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">    <tt class="py-comment"># for the last record copy the  predecessor in sens to it</tt>
 </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">    <tt class="py-comment"># and write 1 to specificity    </tt>
 </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">    <tt class="py-name">spez</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">    <tt class="py-name">sens</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">sens</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">    
 </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">
 </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">    <tt class="py-name">rocarray1</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">sens</tt><tt class="py-op">,</tt><tt class="py-name">spez</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">    <tt class="py-name">rocarray1</tt> <tt class="py-op">=</tt> <tt class="py-name">rocarray1</tt><tt class="py-op">.</tt><tt class="py-name">flatten</tt><tt class="py-op">(</tt><tt class="py-string">'F'</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">    <tt class="py-name">rocarray1</tt><tt class="py-op">=</tt> <tt class="py-name">rocarray1</tt><tt class="py-op">.</tt><tt class="py-name">reshape</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">spez</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">    
 </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">    <tt class="py-name">rocarray</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">sens</tt><tt class="py-op">,</tt><tt class="py-name">spez</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">    <tt class="py-name">rocarray</tt> <tt class="py-op">=</tt> <tt class="py-name">rocarray</tt><tt class="py-op">.</tt><tt class="py-name">flatten</tt><tt class="py-op">(</tt><tt class="py-string">'F'</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">    <tt class="py-name">rocarray</tt> <tt class="py-op">=</tt> <tt class="py-name">rocarray</tt><tt class="py-op">.</tt><tt class="py-name">reshape</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">spez</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">    <tt class="py-name">rocarray</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">sort</tt><tt class="py-op">(</tt><tt class="py-name">rocarray</tt><tt class="py-op">.</tt><tt class="py-name">view</tt><tt class="py-op">(</tt><tt class="py-string">'float,float'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">order</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'f0'</tt><tt class="py-op">,</tt><tt class="py-string">'f1'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">view</tt><tt class="py-op">(</tt><tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">float</tt><tt class="py-op">)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">    
 </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">    <tt class="py-name">rocarrayCorrected</tt> <tt class="py-op">=</tt> <tt class="py-name">rocarray</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">    
 </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">    <tt class="py-comment">#print rocarrayCorrected</tt>
 </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">    <tt class="py-comment"># project points where...</tt>
 </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">m</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rocarrayCorrected</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">            <tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-name">m</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">
 </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">            
 </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">    <tt class="py-comment">#print rocarrayCorrected            </tt>
 </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">hold</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt class="py-number">111</tt><tt class="py-op">)</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">    <tt class="py-comment">#plt.scatter(spez, sens, c='b', marker='o', facecolor='red')</tt>
 </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">    <tt class="py-comment">#plt.plot(rocarray[:,1], rocarray[:,0]</tt>
 </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">marker</tt><tt class="py-op">=</tt><tt class="py-string">'o'</tt><tt class="py-op">,</tt> <tt class="py-name">markersize</tt><tt class="py-op">=</tt><tt class="py-number">7</tt><tt class="py-op">,</tt><tt class="py-name">linestyle</tt><tt class="py-op">=</tt><tt class="py-string">'--'</tt><tt class="py-op">,</tt> <tt class="py-name">color</tt><tt class="py-op">=</tt><tt class="py-string">'r'</tt><tt class="py-op">,</tt> <tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-string">'projected'</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">rocarray1</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">rocarray1</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">linestyle</tt><tt class="py-op">=</tt><tt class="py-string">"None"</tt><tt class="py-op">,</tt><tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-string">'real'</tt><tt class="py-op">,</tt><tt class="py-name">marker</tt><tt class="py-op">=</tt><tt class="py-string">'.'</tt><tt class="py-op">,</tt><tt class="py-name">color</tt><tt class="py-op">=</tt><tt class="py-string">'g'</tt><tt class="py-op">)</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'1-specificity'</tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">ylabel</tt><tt class="py-op">(</tt><tt class="py-string">'sensitivity'</tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">title</tt><tt class="py-op">(</tt><tt class="py-string">r'ROC:'</tt><tt class="py-op">+</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">axis</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">0.1</tt><tt class="py-op">,</tt><tt class="py-number">1.1</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">0.1</tt><tt class="py-op">,</tt><tt class="py-number">1.1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">grid</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">legend</tt><tt class="py-op">(</tt><tt class="py-name">loc</tt><tt class="py-op">=</tt><tt class="py-string">'lower right'</tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">tight_layout</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">savefig</tt><tt class="py-op">(</tt><tt class="py-name">prefix</tt> <tt class="py-op">+</tt> <tt class="py-string">"_ROC.pdf"</tt><tt class="py-op">,</tt><tt class="py-name">format</tt><tt class="py-op">=</tt><tt class="py-string">'pdf'</tt><tt class="py-op">)</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">clf</tt>   </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line">    
 </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">    
 </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">    <tt class="py-name">AUC</tt> <tt class="py-op">=</tt> <tt id="link-0" class="py-name" targets="Function core.PlotData.trapezoidal_rule()=core.PlotData-module.html#trapezoidal_rule"><a title="core.PlotData.trapezoidal_rule" class="py-name" href="#" onclick="return doclink('link-0', 'trapezoidal_rule', 'link-0');">trapezoidal_rule</a></tt><tt class="py-op">(</tt><tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">rocarrayCorrected</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">    
 </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">    <tt class="py-name">fobj</tt> <tt class="py-op">=</tt>  <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">prefix</tt><tt class="py-op">+</tt><tt class="py-string">"_roctable.txt"</tt><tt class="py-op">,</tt><tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">    <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">"RQ\tGAPS\tMM\tPTP\tFP\tP\tSn\t1-Sp\tF\r\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">rocvector</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line">        <tt class="py-name">temp</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">rocvector</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">        <tt class="py-name">tempstr</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">temp</tt><tt class="py-op">)</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">        <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">tempstr</tt><tt class="py-op">+</tt><tt class="py-string">"\r\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line">
 </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">    <tt class="py-name">endtime</tt><tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-op">(</tt><tt class="py-string">"X"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">round</tt><tt class="py-op">(</tt><tt class="py-name">AUC</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">
 </tt>
<a name="plotOverviewHist"></a><div id="plotOverviewHist-def"><a name="L200"></a><tt class="py-lineno">200</tt> <a class="py-toggle" href="#" id="plotOverviewHist-toggle" onclick="return toggle('plotOverviewHist');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="core.PlotData-module.html#plotOverviewHist">plotOverviewHist</a><tt class="py-op">(</tt><tt class="py-param">fp</tt><tt class="py-op">,</tt><tt class="py-param">tp</tt><tt class="py-op">,</tt><tt class="py-param">label</tt><tt class="py-op">,</tt><tt class="py-param">prefix</tt><tt class="py-op">,</tt><tt class="py-param">mappernames</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plotOverviewHist-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plotOverviewHist-expanded"><a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">    <tt class="py-docstring">"""Plots true positives and false positives into 2 different histogram subplots. """</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line">    <tt class="py-name">prefix2</tt> <tt class="py-op">=</tt> <tt class="py-string">"/"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">prefix</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">"/"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">"/"</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">    <tt class="py-name">fobj</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">prefix2</tt><tt class="py-op">+</tt><tt class="py-string">"indexMappingTools.txt"</tt><tt class="py-op">,</tt><tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">label</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">        <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">"%s - %s\r\n"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">mappernames</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">    <tt class="py-name">fobj</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">    
 </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line">    <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">fp</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">3</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">    <tt class="py-name">xmax</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">    <tt class="py-name">ymaxTP</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">tp</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">0.1</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">    <tt class="py-name">ymaxFP</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">fp</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">0.1</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">
 </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">    <tt class="py-comment">##### SUBPLOT NUMBER OF MISMATCHES ####</tt>
 </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line">    <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">tp</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">    <tt class="py-name">x</tt> <tt class="py-op">=</tt><tt class="py-name">x</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">    <tt class="py-name">z</tt> <tt class="py-op">=</tt> <tt class="py-name">fp</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line">
 </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line"> 
 </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line">    <tt class="py-name">fig</tt> <tt class="py-op">=</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line">    <tt class="py-comment"># only plot every 2nd label</tt>
 </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">label</tt><tt class="py-op">)</tt> <tt class="py-op">&lt;=</tt> <tt class="py-number">7</tt><tt class="py-op">:</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line">        <tt class="py-name">widthp</tt> <tt class="py-op">=</tt> <tt class="py-number">0.7</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line">        <tt class="py-name">ticks</tt> <tt class="py-op">=</tt> <tt class="py-name">label</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line">        <tt class="py-name">widthp</tt> <tt class="py-op">=</tt> <tt class="py-number">0.3</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line">        <tt class="py-name">ticks</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt> <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">%</tt><tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-keyword">else</tt> <tt class="py-string">""</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">label</tt><tt class="py-op">]</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line">    <tt class="py-comment"># Here we're adding 2 subplots.  The grid is set</tt>
 </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line">    <tt class="py-comment"># up as one row, two columns.</tt>
 </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line">    <tt class="py-name">ax1</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line">    <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">bar</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-name">width</tt><tt class="py-op">=</tt><tt class="py-name">widthp</tt><tt class="py-op">,</tt> <tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-string">'darkgreen'</tt><tt class="py-op">)</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line">    <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">set_ylabel</tt><tt class="py-op">(</tt><tt class="py-string">'#TP hits'</tt><tt class="py-op">)</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line">    <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">set_xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'index mapping tool'</tt><tt class="py-op">)</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line">    <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">set_title</tt><tt class="py-op">(</tt><tt class="py-string">"Global comparison #TP hits"</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">xticks</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">ticks</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">grid</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">axis</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">xmax</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">ymaxTP</tt><tt class="py-op">+</tt><tt class="py-name">ymaxTP</tt><tt class="py-op">*</tt><tt class="py-number">10</tt><tt class="py-op">/</tt><tt class="py-number">100</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line">    
 </tt>
<a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line">    <tt class="py-comment"># on the second axis, make the width smaller (default is 0.8)</tt>
 </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line">    <tt class="py-name">ax2</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line">    <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">bar</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">z</tt><tt class="py-op">,</tt><tt class="py-name">width</tt><tt class="py-op">=</tt><tt class="py-name">widthp</tt><tt class="py-op">,</tt> <tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-string">'darkred'</tt><tt class="py-op">)</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line">    <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">set_ylabel</tt><tt class="py-op">(</tt><tt class="py-string">'#FP hits'</tt><tt class="py-op">)</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line">    <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">set_xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'index mapping tool'</tt><tt class="py-op">)</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line">    <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">set_title</tt><tt class="py-op">(</tt><tt class="py-string">"Global comparison #FP hits"</tt><tt class="py-op">)</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">axis</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">xmax</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">ymaxFP</tt><tt class="py-op">+</tt><tt class="py-name">ymaxFP</tt><tt class="py-op">*</tt><tt class="py-number">10</tt><tt class="py-op">/</tt><tt class="py-number">100</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">xticks</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">ticks</tt><tt class="py-op">)</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">grid</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">tight_layout</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">savefig</tt><tt class="py-op">(</tt><tt class="py-name">prefix2</tt> <tt class="py-op">+</tt> <tt class="py-string">"Overall_histabs.pdf"</tt><tt class="py-op">,</tt><tt class="py-name">format</tt><tt class="py-op">=</tt><tt class="py-string">'pdf'</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">clf</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line">    
 </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line">    
 </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line">    <tt class="py-name">tpsum</tt> <tt class="py-op">=</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">tp</tt><tt class="py-op">)</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line">    <tt class="py-name">fpsum</tt> <tt class="py-op">=</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">fp</tt><tt class="py-op">)</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line">    <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">tpsum</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">tp</tt><tt class="py-op">]</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line">    <tt class="py-name">x</tt> <tt class="py-op">=</tt><tt class="py-name">x</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line">    <tt class="py-name">z</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">fpsum</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">fp</tt><tt class="py-op">]</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line">    <tt class="py-name">ymax</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">0.2</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line">    
 </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line">    <tt class="py-name">fig</tt> <tt class="py-op">=</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line">    <tt class="py-comment"># only plot every 2nd labelare provided</tt>
 </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">label</tt><tt class="py-op">)</tt> <tt class="py-op">&lt;=</tt> <tt class="py-number">7</tt><tt class="py-op">:</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line">        <tt class="py-name">ticks</tt> <tt class="py-op">=</tt> <tt class="py-name">label</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line">        <tt class="py-name">ticks</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">i</tt> <tt class="py-keyword">if</tt> <tt class="py-name">i</tt><tt class="py-op">%</tt><tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-keyword">else</tt> <tt class="py-string">""</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">label</tt><tt class="py-op">]</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line">    <tt class="py-comment"># Here we're adding 2 subplots.  The grid is set</tt>
 </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line">    <tt class="py-comment"># up as one row, two columns.</tt>
 </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line">    <tt class="py-name">ax1</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line">
 </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line">   
 </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line">    <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">bar</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-name">width</tt><tt class="py-op">=</tt><tt class="py-name">widthp</tt><tt class="py-op">,</tt> <tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-string">'darkgreen'</tt><tt class="py-op">)</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line">    <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">set_ylabel</tt><tt class="py-op">(</tt><tt class="py-string">'%TP hits'</tt><tt class="py-op">)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">    <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">set_xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'index mapping tool'</tt><tt class="py-op">)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line">    <tt class="py-name">ax1</tt><tt class="py-op">.</tt><tt class="py-name">set_title</tt><tt class="py-op">(</tt><tt class="py-string">"Global comparison %TP hits"</tt><tt class="py-op">)</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">xticks</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">ticks</tt><tt class="py-op">)</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">grid</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">axis</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">xmax</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">1.1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line">    
 </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line">    <tt class="py-comment"># on the second axis, make the width smaller (default is 0.8)</tt>
 </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line">    <tt class="py-name">ax2</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line">    <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">bar</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">z</tt><tt class="py-op">,</tt><tt class="py-name">width</tt><tt class="py-op">=</tt><tt class="py-name">widthp</tt><tt class="py-op">,</tt> <tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-string">'darkred'</tt><tt class="py-op">)</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line">    <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">set_ylabel</tt><tt class="py-op">(</tt><tt class="py-string">'%FP hits'</tt><tt class="py-op">)</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line">    <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">set_xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'index mapping tool'</tt><tt class="py-op">)</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line">    <tt class="py-name">ax2</tt><tt class="py-op">.</tt><tt class="py-name">set_title</tt><tt class="py-op">(</tt><tt class="py-string">"Global comparison %FP hits"</tt><tt class="py-op">)</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">axis</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">xmax</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">1.1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">xticks</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">ticks</tt><tt class="py-op">)</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">grid</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line">    <tt class="py-name">plt</tt><tt class="py-op">.</tt><tt class="py-name">tight_layout</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">savefig</tt><tt class="py-op">(</tt><tt class="py-name">prefix2</tt> <tt class="py-op">+</tt> <tt class="py-string">"Overall_histper.pdf"</tt><tt class="py-op">,</tt><tt class="py-name">format</tt><tt class="py-op">=</tt><tt class="py-string">'pdf'</tt><tt class="py-op">)</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line">    <tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">clf</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line">    
 </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-op">(</tt><tt class="py-string">"X"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
</div><a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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