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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Graphics-module.html">Package Graphics</a> ::
<a href="Bio.Graphics.DisplayRepresentation-module.html">Module DisplayRepresentation</a> ::
Class ChromosomeCounts
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class ChromosomeCounts</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">ChromosomeCounts</strong>
</pre>
<hr />
<p>Represent a chromosome with count information.</p>
<p>This is used to display information about counts along a chromosome.
The segments are expected to have different count information, which will
be displayed using a color scheme.</p>
<p>I envision using this class when you think that certain regions of the
chromosome will be especially abundant in the counts, and you want to
pick those out.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">segment_names</span>,
<span class="summary-sig-arg">color_scheme</span>=<span class="summary-sig-default"><code class="variable-group">{</code><code class="variable-group">(</code>1<code class="variable-op">, </code>1<code class="variable-group">)</code><code class="variable-op">: </code>Color(.933333,.509804,.933333)<code class="variable-op">, </code><code class="variable-group">(</code>2<code class="variable-op">, </code>2<code class="variable-group">)</code><code class="variable-op">: </code>Color(.294118<code class="variable-ellipsis">...</code></span>)</span><br />
Initialize a representation of chromosome counts.</td>
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<span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts.__init__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#add_count" class="summary-sig-name">add_count</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">segment_name</span>,
<span class="summary-sig-arg">count</span>=<span class="summary-sig-default">1</span>)</span><br />
Add counts to the given segment name.</td>
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<span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts.add_count">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#scale_segment_value" class="summary-sig-name">scale_segment_value</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">segment_name</span>,
<span class="summary-sig-arg">scale_value</span>=<span class="summary-sig-default">None</span>)</span><br />
Divide the counts for a segment by some kind of scale value.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts.scale_segment_value">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#add_label" class="summary-sig-name">add_label</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">segment_name</span>,
<span class="summary-sig-arg">label</span>)</span><br />
Add a label to a specfic segment.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts.add_label">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#set_scale" class="summary-sig-name">set_scale</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">segment_name</span>,
<span class="summary-sig-arg">scale</span>)</span><br />
Set the scale for a specific chromosome segment.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts.set_scale">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#get_segment_info" class="summary-sig-name">get_segment_info</a>(<span class="summary-sig-arg">self</span>)</span><br />
Retrieve the color and label info about the segments.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts.get_segment_info">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#fill_chromosome" class="summary-sig-name">fill_chromosome</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">chromosome</span>)</span><br />
Add the collected segment information to a chromosome for drawing.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts.fill_chromosome">source code</a></span>
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<td><span class="summary-sig"><a name="_color_from_count"></a><span class="summary-sig-name">_color_from_count</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">count</span>)</span><br />
Translate the given count into a color using the color scheme.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts._color_from_count">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">segment_names</span>,
<span class="sig-arg">color_scheme</span>=<span class="sig-default"><code class="variable-group">{</code><code class="variable-group">(</code>1<code class="variable-op">, </code>1<code class="variable-group">)</code><code class="variable-op">: </code>Color(.933333,.509804,.933333)<code class="variable-op">, </code><code class="variable-group">(</code>2<code class="variable-op">, </code>2<code class="variable-group">)</code><code class="variable-op">: </code>Color(.294118<code class="variable-ellipsis">...</code></span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts.__init__">source code</a></span>
</td>
</tr></table>
<p>Initialize a representation of chromosome counts.</p>
<p>Arguments:</p>
<p>o segment_names - An ordered list of all segment names along the
chromosome. The count and other information will be added to these.</p>
<p>o color_scheme - A coloring scheme to use in the counts. This should
be a dictionary mapping count ranges to colors (specified in
reportlab.lib.colors).</p>
<dl class="fields">
<dt>Overrides:
object.__init__
</dt>
</dl>
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</div>
<a name="add_count"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">add_count</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">segment_name</span>,
<span class="sig-arg">count</span>=<span class="sig-default">1</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts.add_count">source code</a></span>
</td>
</tr></table>
<p>Add counts to the given segment name.</p>
<p>Arguments:</p>
<p>o segment_name - The name of the segment we should add counts to. If
the name is not present, a KeyError will be raised.</p>
<p>o count - The counts to add the current segment. This defaults to a
single count.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="scale_segment_value"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">scale_segment_value</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">segment_name</span>,
<span class="sig-arg">scale_value</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts.scale_segment_value">source code</a></span>
</td>
</tr></table>
<p>Divide the counts for a segment by some kind of scale value.</p>
<p>This is useful if segments aren't represented by raw counts, but are
instead counts divided by some number.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="add_label"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">add_label</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">segment_name</span>,
<span class="sig-arg">label</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts.add_label">source code</a></span>
</td>
</tr></table>
<p>Add a label to a specfic segment.</p>
<p>Raises a KeyError is the specified segment name is not found.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="set_scale"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">set_scale</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">segment_name</span>,
<span class="sig-arg">scale</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts.set_scale">source code</a></span>
</td>
</tr></table>
<p>Set the scale for a specific chromosome segment.</p>
<p>By default all segments have the same scale -- this allows scaling by
the size of the segment.</p>
<p>Raises a KeyError is the specified segment name is not found.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="get_segment_info"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_segment_info</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts.get_segment_info">source code</a></span>
</td>
</tr></table>
<p>Retrieve the color and label info about the segments.</p>
<p>Returns a list consiting of two tuples specifying the counts and label
name for each segment. The list is ordered according to the original
listing of names. Labels are set as None if no label was specified.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="fill_chromosome"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">fill_chromosome</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">chromosome</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.DisplayRepresentation-pysrc.html#ChromosomeCounts.fill_chromosome">source code</a></span>
</td>
</tr></table>
<p>Add the collected segment information to a chromosome for drawing.</p>
<p>Arguments:</p>
<p>o chromosome - A Chromosome graphics object that we can add chromosome
segments to.</p>
<p>This creates ChromosomeSegment (and TelomereSegment) objects to fill
in the chromosome. The information is derived from the label and count
information, with counts transformed to the specified color map.</p>
<p>Returns the chromosome with all of the segments added.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
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