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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.GenomeDiagram-module.html">Package GenomeDiagram</a> ::
<a href="Bio.Graphics.GenomeDiagram._GraphSet-module.html" onclick="show_private();">Module _GraphSet</a> ::
Class GraphSet
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class GraphSet</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">GraphSet</strong>
</pre>
<hr />
<pre class="literalblock">
GraphSet
Provides:
Methods:
o __init__(self, set_id=None, name=None) Called on instantiation
o new_graph(self, data, name, style='bar', color=colors.lightgreen,
altcolor=colors.darkseagreen) Create new graph in the set
from the passed data, with the passed parameters
o del_graph(self, graph_id) Delete graph with the passed id
o get_graphs(self) Returns a list of all graphs
o get_ids(self) Returns a list of graph ids
o range(self) Returns the range covered by the graphs in the set
o to_string(self, verbose=0) Returns a string describing the set
o __len__(self) Returns the length of sequence covered by the set
o __getitem__(self, key) Returns the graph with the id of the passed key
o __str__(self) Returns a string describing the set
Attributes:
o id Unique identifier for the set
o name String describing the set
</pre>
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<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>=<span class="summary-sig-default">None</span>)</span><br />
o name String identifying the graph set sensibly</td>
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<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.__init__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#new_graph" class="summary-sig-name">new_graph</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">data</span>,
<span class="summary-sig-arg">name</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">style</span>=<span class="summary-sig-default">'bar'</span>,
<span class="summary-sig-arg">color</span>=<span class="summary-sig-default">colors.lightgreen</span>,
<span class="summary-sig-arg">altcolor</span>=<span class="summary-sig-default">colors.darkseagreen</span>)</span><br />
o data List of (position, value) int tuples</td>
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<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.new_graph">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.GenomeDiagram._GraphSet.GraphSet-class.html#del_graph" class="summary-sig-name">del_graph</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">graph_id</span>)</span><br />
o graph_id Identifying value of the graph</td>
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<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.del_graph">source code</a></span>
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<span class="summary-type">[Graph, Graph, ...]</span>
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<td><span class="summary-sig"><a name="get_graphs"></a><span class="summary-sig-name">get_graphs</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return a list of all graphs in the graph set, sorted by id (for
reliable stacking...)</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.get_graphs">source code</a></span>
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<span class="summary-type">[int, int, ...]</span>
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<td><span class="summary-sig"><a name="get_ids"></a><span class="summary-sig-name">get_ids</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return a list of all ids for the graph set</td>
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<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.get_ids">source code</a></span>
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<span class="summary-type">(int, int)</span>
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<td><span class="summary-sig"><a name="range"></a><span class="summary-sig-name">range</span>(<span class="summary-sig-arg">self</span>)</span><br />
Returns the lowest and highest base (or mark) numbers as a tuple</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.range">source code</a></span>
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<span class="summary-type">(float, float, float, float, float)</span>
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<td><span class="summary-sig"><a name="data_quartiles"></a><span class="summary-sig-name">data_quartiles</span>(<span class="summary-sig-arg">self</span>)</span><br />
Returns the (minimum, lowerQ, medianQ, upperQ, maximum) values as a
tuple</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.data_quartiles">source code</a></span>
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<span class="summary-type">""</span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#to_string" class="summary-sig-name">to_string</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">verbose</span>=<span class="summary-sig-default">0</span>)</span><br />
o verbose Flag indicating whether a short or complete account
of the set is required</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.to_string">source code</a></span>
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<span class="summary-type">int</span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="__len__"></a><span class="summary-sig-name">__len__</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return the number of graphs in the set</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.__len__">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">Graph</span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="__getitem__"></a><span class="summary-sig-name">__getitem__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span><br />
Return a graph, keyed by id</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.__getitem__">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">""</span>
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<td><span class="summary-sig"><a href="Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns a formatted string with information about the feature set</td>
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<span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.__str__">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>__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">name</span>=<span class="sig-default">None</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.__init__">source code</a></span>
</td>
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<p>o name String identifying the graph set sensibly</p>
<dl class="fields">
<dt>Overrides:
object.__init__
</dt>
</dl>
</td></tr></table>
</div>
<a name="new_graph"></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">new_graph</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">data</span>,
<span class="sig-arg">name</span>=<span class="sig-default">None</span>,
<span class="sig-arg">style</span>=<span class="sig-default">'bar'</span>,
<span class="sig-arg">color</span>=<span class="sig-default">colors.lightgreen</span>,
<span class="sig-arg">altcolor</span>=<span class="sig-default">colors.darkseagreen</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.new_graph">source code</a></span>
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<pre class="literalblock">
o data List of (position, value) int tuples
o name String, description of the graph
o style String ('bar', 'heat', 'line') describing how the graph
will be drawn
o color colors.Color describing the color to draw all or 'high'
(some styles) data (overridden by backwards compatible
argument with UK spelling, colour).
o altcolor colors.Color describing the color to draw 'low' (some
styles) data (overridden by backwards compatible argument
with UK spelling, colour).
o linewidth Float describing linewidth for graph
o center Float setting the value at which the x-axis
crosses the y-axis (overridden by backwards
compatible argument with UK spelling, centre)
Add a GraphData object to the diagram (will be stored
internally
</pre>
<dl class="fields">
</dl>
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</div>
<a name="del_graph"></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">del_graph</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">graph_id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.del_graph">source code</a></span>
</td>
</tr></table>
<p>o graph_id Identifying value of the graph</p>
<p>Remove a graph from the set, indicated by its id</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="to_string"></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">to_string</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">verbose</span>=<span class="sig-default">0</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.to_string">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
o verbose Flag indicating whether a short or complete account
of the set is required
Returns a formatted string with information about the set
</pre>
<dl class="fields">
<dt>Returns: ""</dt>
</dl>
</td></tr></table>
</div>
<a name="__str__"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__str__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Informal representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-pysrc.html#GraphSet.__str__">source code</a></span>
</td>
</tr></table>
<p>Returns a formatted string with information about the feature set</p>
<dl class="fields">
<dt>Returns: ""</dt>
<dt>Overrides:
object.__str__
</dt>
</dl>
</td></tr></table>
</div>
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