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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Graphics-module.html">Package Graphics</a> ::
Module Comparative
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<h1 class="epydoc">Source Code for <a href="Bio.Graphics.Comparative-module.html">Module Bio.Graphics.Comparative</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Plots to compare information between different sources.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">This file contains high level plots which are designed to be used to</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">compare different types of information. The most basic example is comparing</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">two variables in a traditional scatter plot.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"># reportlab</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt class="py-name">reportlab</tt><tt class="py-op">.</tt><tt class="py-name">pdfgen</tt> <tt class="py-keyword">import</tt> <tt class="py-name">canvas</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">reportlab</tt><tt class="py-op">.</tt><tt class="py-name">lib</tt> <tt class="py-keyword">import</tt> <tt class="py-name">colors</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">reportlab</tt><tt class="py-op">.</tt><tt class="py-name">graphics</tt><tt class="py-op">.</tt><tt class="py-name">charts</tt><tt class="py-op">.</tt><tt class="py-name">lineplots</tt> <tt class="py-keyword">import</tt> <tt class="py-name">LinePlot</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">reportlab</tt><tt class="py-op">.</tt><tt class="py-name">lib</tt><tt class="py-op">.</tt><tt class="py-name">pagesizes</tt> <tt class="py-keyword">import</tt> <tt class="py-name">letter</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">reportlab</tt><tt class="py-op">.</tt><tt class="py-name">lib</tt><tt class="py-op">.</tt><tt class="py-name">units</tt> <tt class="py-keyword">import</tt> <tt class="py-name">inch</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">reportlab</tt><tt class="py-op">.</tt><tt class="py-name">graphics</tt><tt class="py-op">.</tt><tt class="py-name">shapes</tt> <tt class="py-keyword">import</tt> <tt class="py-name">Drawing</tt><tt class="py-op">,</tt> <tt id="link-0" class="py-name" targets="Class Bio.Decode.String=Bio.Decode.String-class.html"><a title="Bio.Decode.String" class="py-name" href="#" onclick="return doclink('link-0', 'String', 'link-0');">String</a></tt><tt class="py-op">,</tt> <tt id="link-1" class="py-name" targets="Class Martel.Expression.Group=Martel.Expression.Group-class.html,Function Martel.Group()=Martel-module.html#Group"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-1', 'Group', 'link-1');">Group</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">reportlab</tt><tt class="py-op">.</tt><tt class="py-name">graphics</tt> <tt class="py-keyword">import</tt> <tt class="py-name">renderPDF</tt><tt class="py-op">,</tt> <tt class="py-name">renderPS</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">reportlab</tt><tt class="py-op">.</tt><tt class="py-name">graphics</tt><tt class="py-op">.</tt><tt class="py-name">charts</tt><tt class="py-op">.</tt><tt class="py-name">markers</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> </tt>
<a name="ComparativeScatterPlot"></a><div id="ComparativeScatterPlot-def"><a name="L18"></a><tt class="py-lineno"> 18</tt> <a class="py-toggle" href="#" id="ComparativeScatterPlot-toggle" onclick="return toggle('ComparativeScatterPlot');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Graphics.Comparative.ComparativeScatterPlot-class.html">ComparativeScatterPlot</a><tt class="py-op">:</tt> </tt>
</div><div id="ComparativeScatterPlot-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ComparativeScatterPlot-expanded"><a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-docstring">"""Display a scatter-type plot comparing two different kinds of info.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> Attributes;</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> o display_info -- a 2D list of the information we'll be outputting. Each</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> top level list is a different data type, and each data point is a two-tuple</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> of the coordinates of a point. So if you had two distributions of points,</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> it should look like:</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> display_info = [[(1, 2), (3, 4)],</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> [(5, 6), (7, 8)]]</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> if everything is just one set of points, display_info can look like:</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> display_info = [[(1, 2), (3, 4), (5, 6)]]</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="ComparativeScatterPlot.__init__"></a><div id="ComparativeScatterPlot.__init__-def"><a name="L35"></a><tt class="py-lineno"> 35</tt> <a class="py-toggle" href="#" id="ComparativeScatterPlot.__init__-toggle" onclick="return toggle('ComparativeScatterPlot.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.Comparative.ComparativeScatterPlot-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">output_format</tt> <tt class="py-op">=</tt> <tt class="py-string">'pdf'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ComparativeScatterPlot.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ComparativeScatterPlot.__init__-expanded"><a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-comment"># customizable attributes</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">number_of_columns</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">page_size</tt> <tt class="py-op">=</tt> <tt class="py-name">letter</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">title_size</tt> <tt class="py-op">=</tt> <tt class="py-number">20</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">output_format</tt> <tt class="py-op">=</tt> <tt class="py-name">output_format</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-comment"># the information we'll be writing</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">display_info</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-comment"># inital colors and shapes used for drawing points</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color_choices</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">red</tt><tt class="py-op">,</tt> <tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">green</tt><tt class="py-op">,</tt> <tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">blue</tt><tt class="py-op">,</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">yellow</tt><tt class="py-op">,</tt> <tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">orange</tt><tt class="py-op">,</tt> <tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">black</tt><tt class="py-op">]</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">shape_choices</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">makeFilledCircle</tt><tt class="py-op">,</tt> <tt class="py-name">makeEmptySquare</tt><tt class="py-op">,</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">makeFilledDiamond</tt><tt class="py-op">,</tt> <tt class="py-name">makeFilledSquare</tt><tt class="py-op">,</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">makeEmptyCircle</tt><tt class="py-op">,</tt> <tt class="py-name">makeSmiley</tt><tt class="py-op">]</tt> </tt>
</div><a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> </tt>
<a name="ComparativeScatterPlot.draw_to_file"></a><div id="ComparativeScatterPlot.draw_to_file-def"><a name="L53"></a><tt class="py-lineno"> 53</tt> <a class="py-toggle" href="#" id="ComparativeScatterPlot.draw_to_file-toggle" onclick="return toggle('ComparativeScatterPlot.draw_to_file');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.Comparative.ComparativeScatterPlot-class.html#draw_to_file">draw_to_file</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">output_file</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ComparativeScatterPlot.draw_to_file-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ComparativeScatterPlot.draw_to_file-expanded"><a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-docstring">"""Write the comparative plot to a file.</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-name">width</tt><tt class="py-op">,</tt> <tt class="py-name">height</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">page_size</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">cur_drawing</tt> <tt class="py-op">=</tt> <tt class="py-name">Drawing</tt><tt class="py-op">(</tt><tt class="py-name">width</tt><tt class="py-op">,</tt> <tt class="py-name">height</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.Graphics.BasicChromosome.Organism._draw_title()=Bio.Graphics.BasicChromosome.Organism-class.html#_draw_title,Method Bio.Graphics.Comparative.ComparativeScatterPlot._draw_title()=Bio.Graphics.Comparative.ComparativeScatterPlot-class.html#_draw_title,Method Bio.Graphics.Distribution.BarChartDistribution._draw_title()=Bio.Graphics.Distribution.BarChartDistribution-class.html#_draw_title,Method Bio.Graphics.Distribution.DistributionPage._draw_title()=Bio.Graphics.Distribution.DistributionPage-class.html#_draw_title"><a title="Bio.Graphics.BasicChromosome.Organism._draw_title
Bio.Graphics.Comparative.ComparativeScatterPlot._draw_title
Bio.Graphics.Distribution.BarChartDistribution._draw_title
Bio.Graphics.Distribution.DistributionPage._draw_title" class="py-name" href="#" onclick="return doclink('link-2', '_draw_title', 'link-2');">_draw_title</a></tt><tt class="py-op">(</tt><tt class="py-name">cur_drawing</tt><tt class="py-op">,</tt> <tt id="link-3" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.title()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#title,Method Bio.GenBank._FeatureConsumer.title()=Bio.GenBank._FeatureConsumer-class.html#title,Method Bio.GenBank._RecordConsumer.title()=Bio.GenBank._RecordConsumer-class.html#title,Method Bio.Medline._RecordConsumer.title()=Bio.Medline._RecordConsumer-class.html#title,Variable Bio.expressions.fasta.title=Bio.expressions.fasta-module.html#title"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-3', 'title', 'link-3');">title</a></tt><tt class="py-op">,</tt> <tt class="py-name">width</tt><tt class="py-op">,</tt> <tt class="py-name">height</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 class="py-name">start_x</tt> <tt class="py-op">=</tt> <tt class="py-name">inch</tt> <tt class="py-op">*</tt> <tt class="py-number">.5</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">end_x</tt> <tt class="py-op">=</tt> <tt class="py-name">width</tt> <tt class="py-op">-</tt> <tt class="py-name">inch</tt> <tt class="py-op">*</tt> <tt class="py-number">.5</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">end_y</tt> <tt class="py-op">=</tt> <tt class="py-name">height</tt> <tt class="py-op">-</tt> <tt class="py-number">1.5</tt> <tt class="py-op">*</tt> <tt class="py-name">inch</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">start_y</tt> <tt class="py-op">=</tt> <tt class="py-number">.5</tt> <tt class="py-op">*</tt> <tt class="py-name">inch</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.Graphics.Comparative.ComparativeScatterPlot._draw_scatter_plot()=Bio.Graphics.Comparative.ComparativeScatterPlot-class.html#_draw_scatter_plot"><a title="Bio.Graphics.Comparative.ComparativeScatterPlot._draw_scatter_plot" class="py-name" href="#" onclick="return doclink('link-4', '_draw_scatter_plot', 'link-4');">_draw_scatter_plot</a></tt><tt class="py-op">(</tt><tt class="py-name">cur_drawing</tt><tt class="py-op">,</tt> <tt class="py-name">start_x</tt><tt class="py-op">,</tt> <tt class="py-name">start_y</tt><tt class="py-op">,</tt> <tt class="py-name">end_x</tt><tt class="py-op">,</tt> <tt class="py-name">end_y</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">output_format</tt> <tt class="py-op">==</tt> <tt class="py-string">'pdf'</tt><tt class="py-op">:</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">out_canvas</tt> <tt class="py-op">=</tt> <tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">Canvas</tt><tt class="py-op">(</tt><tt class="py-name">output_file</tt><tt class="py-op">,</tt> <tt class="py-name">pagesize</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">page_size</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">renderPDF</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.Graphics.BasicChromosome.Chromosome.draw()=Bio.Graphics.BasicChromosome.Chromosome-class.html#draw,Method Bio.Graphics.BasicChromosome.ChromosomeSegment.draw()=Bio.Graphics.BasicChromosome.ChromosomeSegment-class.html#draw,Method Bio.Graphics.BasicChromosome.Organism.draw()=Bio.Graphics.BasicChromosome.Organism-class.html#draw,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.draw()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#draw,Method Bio.Graphics.Distribution.BarChartDistribution.draw()=Bio.Graphics.Distribution.BarChartDistribution-class.html#draw,Method Bio.Graphics.Distribution.DistributionPage.draw()=Bio.Graphics.Distribution.DistributionPage-class.html#draw,Method Bio.Graphics.Distribution.LineDistribution.draw()=Bio.Graphics.Distribution.LineDistribution-class.html#draw"><a title="Bio.Graphics.BasicChromosome.Chromosome.draw
Bio.Graphics.BasicChromosome.ChromosomeSegment.draw
Bio.Graphics.BasicChromosome.Organism.draw
Bio.Graphics.BasicChromosome._ChromosomeComponent.draw
Bio.Graphics.Distribution.BarChartDistribution.draw
Bio.Graphics.Distribution.DistributionPage.draw
Bio.Graphics.Distribution.LineDistribution.draw" class="py-name" href="#" onclick="return doclink('link-5', 'draw', 'link-5');">draw</a></tt><tt class="py-op">(</tt><tt class="py-name">cur_drawing</tt><tt class="py-op">,</tt> <tt class="py-name">out_canvas</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>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-name">out_canvas</tt><tt class="py-op">.</tt><tt class="py-name">showPage</tt><tt class="py-op">(</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">out_canvas</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.Cluster.Record.save()=Bio.Cluster.Record-class.html#save,Function Bio.MarkovModel.save()=Bio.MarkovModel-module.html#save,Method Bio.PDB.PDBIO'.PDBIO.save()=Bio.PDB.PDBIO%27.PDBIO-class.html#save"><a title="Bio.Cluster.Record.save
Bio.MarkovModel.save
Bio.PDB.PDBIO'.PDBIO.save" class="py-name" href="#" onclick="return doclink('link-6', 'save', 'link-6');">save</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">output_format</tt> <tt class="py-op">==</tt> <tt class="py-string">'eps'</tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">renderPS</tt><tt class="py-op">.</tt><tt class="py-name">drawToFile</tt><tt class="py-op">(</tt><tt class="py-name">cur_drawing</tt><tt class="py-op">,</tt> <tt class="py-name">output_file</tt><tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Invalid output format %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">output_format</tt><tt class="py-op">)</tt> </tt>
</div><a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> </tt>
<a name="ComparativeScatterPlot._draw_title"></a><div id="ComparativeScatterPlot._draw_title-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="ComparativeScatterPlot._draw_title-toggle" onclick="return toggle('ComparativeScatterPlot._draw_title');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.Comparative.ComparativeScatterPlot-class.html#_draw_title">_draw_title</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cur_drawing</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">,</tt> <tt class="py-param">width</tt><tt class="py-op">,</tt> <tt class="py-param">height</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ComparativeScatterPlot._draw_title-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ComparativeScatterPlot._draw_title-expanded"><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-docstring">"""Add a title to the page we are outputting.</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">title_string</tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="Bio.Decode.String" class="py-name" href="#" onclick="return doclink('link-7', 'String', 'link-0');">String</a></tt><tt class="py-op">(</tt><tt class="py-name">width</tt> <tt class="py-op">/</tt> <tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-name">height</tt> <tt class="py-op">-</tt> <tt class="py-name">inch</tt><tt class="py-op">,</tt> <tt id="link-8" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-8', 'title', 'link-3');">title</a></tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">title_string</tt><tt class="py-op">.</tt><tt class="py-name">fontName</tt> <tt class="py-op">=</tt> <tt class="py-string">'Helvetica-Bold'</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">title_string</tt><tt class="py-op">.</tt><tt class="py-name">fontSize</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">title_size</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">title_string</tt><tt class="py-op">.</tt><tt class="py-name">textAnchor</tt> <tt class="py-op">=</tt> <tt class="py-string">"middle"</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">cur_drawing</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Variable Bio.Affy.CelFile.add=Bio.Affy.CelFile-module.html#add,Method Bio.EUtils.POM.ElementNode.add()=Bio.EUtils.POM.ElementNode-class.html#add,Method Bio.GFF.easy.Location.add()=Bio.GFF.easy.Location-class.html#add,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.add()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#add,Variable Bio.LogisticRegression.add=Bio.LogisticRegression-module.html#add,Variable Bio.MarkovModel.add=Bio.MarkovModel-module.html#add,Variable Bio.MaxEntropy.add=Bio.MaxEntropy-module.html#add,Variable Bio.NaiveBayes.add=Bio.NaiveBayes-module.html#add,Method Bio.Nexus.Nexus.StepMatrix.add()=Bio.Nexus.Nexus.StepMatrix-class.html#add,Method Bio.Nexus.Nodes.Chain.add()=Bio.Nexus.Nodes.Chain-class.html#add,Method Bio.PDB.Entity.Entity.add()=Bio.PDB.Entity.Entity-class.html#add,Method Bio.PDB.Residue.DisorderedResidue.add()=Bio.PDB.Residue.DisorderedResidue-class.html#add,Method Bio.PDB.Residue.Residue.add()=Bio.PDB.Residue.Residue-class.html#add,Method Bio.Pathway.Rep.HashSet.HashSet.add()=Bio.Pathway.Rep.HashSet.HashSet-class.html#add,Method Bio.Restriction.Restriction.RestrictionBatch.add()=Bio.Restriction.Restriction.RestrictionBatch-class.html#add,Variable Bio.Statistics.lowess.add=Bio.Statistics.lowess-module.html#add,Method Bio.config.FormatRegistry.FormatGroup.add()=Bio.config.FormatRegistry.FormatGroup-class.html#add,Method Bio.config.Registry.RegisterableGroup.add()=Bio.config.Registry.RegisterableGroup-class.html#add,Variable Bio.distance.add=Bio.distance-module.html#add,Variable Bio.kNN.add=Bio.kNN-module.html#add,Method Martel.Dispatch.MulticallEnd.add()=Martel.Dispatch.MulticallEnd-class.html#add,Method Martel.Dispatch.MulticallStart.add()=Martel.Dispatch.MulticallStart-class.html#add"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-9', 'add', 'link-9');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">title_string</tt><tt class="py-op">)</tt> </tt>
</div><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="ComparativeScatterPlot._draw_scatter_plot"></a><div id="ComparativeScatterPlot._draw_scatter_plot-def"><a name="L87"></a><tt class="py-lineno"> 87</tt> <a class="py-toggle" href="#" id="ComparativeScatterPlot._draw_scatter_plot-toggle" onclick="return toggle('ComparativeScatterPlot._draw_scatter_plot');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.Comparative.ComparativeScatterPlot-class.html#_draw_scatter_plot">_draw_scatter_plot</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cur_drawing</tt><tt class="py-op">,</tt> <tt class="py-param">x_start</tt><tt class="py-op">,</tt> <tt class="py-param">y_start</tt><tt class="py-op">,</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-param">x_end</tt><tt class="py-op">,</tt> <tt class="py-param">y_end</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ComparativeScatterPlot._draw_scatter_plot-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ComparativeScatterPlot._draw_scatter_plot-expanded"><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-docstring">"""Draw a scatter plot on the drawing with the given coordinates.</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">scatter_plot</tt> <tt class="py-op">=</tt> <tt class="py-name">LinePlot</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-comment"># set the dimensions of the scatter plot</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">scatter_plot</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-10', 'x', 'link-10');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">x_start</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">scatter_plot</tt><tt class="py-op">.</tt><tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">y_start</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">scatter_plot</tt><tt class="py-op">.</tt><tt class="py-name">width</tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name" targets="Method Bio.FSSP.FSSPAlignDict.abs()=Bio.FSSP.FSSPAlignDict-class.html#abs"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-11', 'abs', 'link-11');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">x_start</tt> <tt class="py-op">-</tt> <tt class="py-name">x_end</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">scatter_plot</tt><tt class="py-op">.</tt><tt class="py-name">height</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-12', 'abs', 'link-11');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">y_start</tt> <tt class="py-op">-</tt> <tt class="py-name">y_end</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">scatter_plot</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-13', 'data', 'link-13');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">display_info</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">scatter_plot</tt><tt class="py-op">.</tt><tt class="py-name">joinedLines</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </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-comment"># set the axes of the plot</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">x_min</tt><tt class="py-op">,</tt> <tt class="py-name">x_max</tt><tt class="py-op">,</tt> <tt class="py-name">y_min</tt><tt class="py-op">,</tt> <tt class="py-name">y_max</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Method Bio.Graphics.Comparative.ComparativeScatterPlot._find_min_max()=Bio.Graphics.Comparative.ComparativeScatterPlot-class.html#_find_min_max"><a title="Bio.Graphics.Comparative.ComparativeScatterPlot._find_min_max" class="py-name" href="#" onclick="return doclink('link-14', '_find_min_max', 'link-14');">_find_min_max</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">display_info</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">scatter_plot</tt><tt class="py-op">.</tt><tt class="py-name">xValueAxis</tt><tt class="py-op">.</tt><tt class="py-name">valueMin</tt> <tt class="py-op">=</tt> <tt class="py-name">x_min</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">scatter_plot</tt><tt class="py-op">.</tt><tt class="py-name">xValueAxis</tt><tt class="py-op">.</tt><tt class="py-name">valueMax</tt> <tt class="py-op">=</tt> <tt class="py-name">x_max</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">scatter_plot</tt><tt class="py-op">.</tt><tt class="py-name">xValueAxis</tt><tt class="py-op">.</tt><tt class="py-name">valueStep</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">x_max</tt> <tt class="py-op">-</tt> <tt class="py-name">x_min</tt><tt class="py-op">)</tt> <tt class="py-op">/</tt> <tt class="py-number">10.0</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">scatter_plot</tt><tt class="py-op">.</tt><tt class="py-name">yValueAxis</tt><tt class="py-op">.</tt><tt class="py-name">valueMin</tt> <tt class="py-op">=</tt> <tt class="py-name">y_min</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-name">scatter_plot</tt><tt class="py-op">.</tt><tt class="py-name">yValueAxis</tt><tt class="py-op">.</tt><tt class="py-name">valueMax</tt> <tt class="py-op">=</tt> <tt class="py-name">y_max</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">scatter_plot</tt><tt class="py-op">.</tt><tt class="py-name">yValueAxis</tt><tt class="py-op">.</tt><tt class="py-name">valueStep</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">y_max</tt> <tt class="py-op">-</tt> <tt class="py-name">y_min</tt><tt class="py-op">)</tt> <tt class="py-op">/</tt> <tt class="py-number">10.0</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.Graphics.Comparative.ComparativeScatterPlot._set_colors_and_shapes()=Bio.Graphics.Comparative.ComparativeScatterPlot-class.html#_set_colors_and_shapes"><a title="Bio.Graphics.Comparative.ComparativeScatterPlot._set_colors_and_shapes" class="py-name" href="#" onclick="return doclink('link-15', '_set_colors_and_shapes', 'link-15');">_set_colors_and_shapes</a></tt><tt class="py-op">(</tt><tt class="py-name">scatter_plot</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">display_info</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">cur_drawing</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-16', 'add', 'link-9');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">scatter_plot</tt><tt class="py-op">)</tt> </tt>
</div><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="ComparativeScatterPlot._set_colors_and_shapes"></a><div id="ComparativeScatterPlot._set_colors_and_shapes-def"><a name="L117"></a><tt class="py-lineno">117</tt> <a class="py-toggle" href="#" id="ComparativeScatterPlot._set_colors_and_shapes-toggle" onclick="return toggle('ComparativeScatterPlot._set_colors_and_shapes');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.Comparative.ComparativeScatterPlot-class.html#_set_colors_and_shapes">_set_colors_and_shapes</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">scatter_plot</tt><tt class="py-op">,</tt> <tt class="py-param">display_info</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ComparativeScatterPlot._set_colors_and_shapes-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ComparativeScatterPlot._set_colors_and_shapes-expanded"><a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-docstring">"""Set the colors and shapes of the points displayed.</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"> By default this just sets all of the points according to the order</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"> of colors and shapes defined in self.color_choices and</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> self.shape_choices. The first 5 shapes and colors are unique, the</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> rest of them are just set to the same color and shape (since I</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> ran out of shapes!).</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> You can change how this function works by either changing the</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> values of the color_choices and shape_choices attributes, or</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> by inheriting from this class and overriding this function.</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">value_num</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">display_info</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-comment"># if we have unique colors, add them</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">value_num</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">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color_choices</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">scatter_plot</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">[</tt><tt class="py-name">value_num</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strokeColor</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color_choices</tt><tt class="py-op">[</tt><tt class="py-name">value_num</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">scatter_plot</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">[</tt><tt class="py-name">value_num</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">symbol</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">shape_choices</tt><tt class="py-op">[</tt><tt class="py-name">value_num</tt><tt class="py-op">]</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-comment"># otherwise just use the last number</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-name">scatter_plot</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">[</tt><tt class="py-name">value_num</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strokeColor</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color_choices</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</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">scatter_plot</tt><tt class="py-op">.</tt><tt class="py-name">lines</tt><tt class="py-op">[</tt><tt class="py-name">value_num</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">symbol</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">shape_choices</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
</div><a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> </tt>
<a name="ComparativeScatterPlot._find_min_max"></a><div id="ComparativeScatterPlot._find_min_max-def"><a name="L144"></a><tt class="py-lineno">144</tt> <a class="py-toggle" href="#" id="ComparativeScatterPlot._find_min_max-toggle" onclick="return toggle('ComparativeScatterPlot._find_min_max');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.Comparative.ComparativeScatterPlot-class.html#_find_min_max">_find_min_max</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">info</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ComparativeScatterPlot._find_min_max-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ComparativeScatterPlot._find_min_max-expanded"><a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-docstring">"""Find the min and max for the x and y coordinates in the given data.</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">x_min</tt> <tt class="py-op">=</tt> <tt class="py-name">info</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">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">x_max</tt> <tt class="py-op">=</tt> <tt class="py-name">info</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">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">y_min</tt> <tt class="py-op">=</tt> <tt class="py-name">info</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">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">y_max</tt> <tt class="py-op">=</tt> <tt class="py-name">info</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">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">two_d_list</tt> <tt class="py-keyword">in</tt> <tt class="py-name">info</tt><tt class="py-op">:</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-17" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-17', 'x', 'link-10');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt> <tt class="py-keyword">in</tt> <tt class="py-name">two_d_list</tt><tt class="py-op">:</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-18" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-18', 'x', 'link-10');">x</a></tt> <tt class="py-op">></tt> <tt class="py-name">x_max</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">x_max</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-19', 'x', 'link-10');">x</a></tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-20" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-20', 'x', 'link-10');">x</a></tt> <tt class="py-op"><</tt> <tt class="py-name">x_min</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">x_min</tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-21', 'x', 'link-10');">x</a></tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">y</tt> <tt class="py-op">></tt> <tt class="py-name">y_max</tt><tt class="py-op">:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">y_max</tt> <tt class="py-op">=</tt> <tt class="py-name">y</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">y</tt> <tt class="py-op"><</tt> <tt class="py-name">y_min</tt><tt class="py-op">:</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">y_min</tt> <tt class="py-op">=</tt> <tt class="py-name">y</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">x_min</tt><tt class="py-op">,</tt> <tt class="py-name">x_max</tt><tt class="py-op">,</tt> <tt class="py-name">y_min</tt><tt class="py-op">,</tt> <tt class="py-name">y_max</tt> </tt>
</div></div><a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> </tt><script type="text/javascript">
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