merged

docs/_build_html/_sources/clustergrammer_js.rst.txt

@@ -53,7 +53,64 @@ The page `multiple_clust.html`_ and corresponding script `load_multiple_clusterg
 
 Clustergrammer-JS API
 =====================
-Clustergrammer-JS' API allows users to pass options to the front-end visualization, such as optional callback functions.
+
+.. js:class:: Clustergrammer(args)
+
+  The Clusterrammer JavaScript object takes the ``args`` object and produces a visualization on the page.
+
+  This ``args`` object has two requried arguments, ``network_data`` and ``root``:
+
+    .. js:attribute:: args.network_data
+
+      This required attribute is where the visualization JSON should be passed as a JavaScript object.
+
+    .. js:attribute:: args.root
+
+      This required attribute is the ``id`` (passed as a string) of the container where Clustergrammer will be built. Each Clustergrammer visualization in a page should be passed a unique ``id``.
+
+    .. js:attribute:: args.about
+
+      This attribute is a string (which can include HTML) that will produce a small about section at the top of the sidebar. This can be used to provide a quick description about the data or visualization.
+
+    .. js:attribute:: args.row_tip_callback
+
+      Users can pass a callback function that will run when mousing over row labels.
+
+    .. js:attribute:: args.col_tip_callback
+
+      Users can pass a callback function that will run when mousing over col labels.
+
+    .. js:attribute:: args.tile_tip_callback
+
+      Users can pass a callback function that will run when mousing over a matrix-cell (e.g. matrix tile).
+
+    .. js:attribute:: args.dendro_callback
+
+      Users can pass a callback function that will run when mousing over a dendrogram cluster (e.g. gray trapezoid)
+
+    .. js:attribute:: args.matrix_update_callback
+
+      Users can pass a callback function that will run anytime the matrix has been updated, for instance when filtering/unfiltering, cropping, etc.
+
+    .. js:attribute:: args.sidebar_width:
+
+      Users can modify the width of the sidebar by specifying the width of the sidebar in pixels as a number.
+
+    .. js:attribute:: args.ini_view
+
+      Users can initialize the 'view' of their matrix, e.g. a initialize the matrix at a particular row filtering level.
+
+  Clustergrammer's attributes and functions are listed below:
+
+  .. js:function:: update_cats(row_data)
+
+    Update the visualization row categories.
+
+    :param row_data: The row category data that will be used to ...
+
+    :param resize_viz: Call this function to resize the visualization to fit in its resized container (if the user has resized the container).
+
+
 
 .. _visualization_json:
 

docs/_build_html/_sources/clustergrammer_js.txt

@@ -53,7 +53,64 @@ The page `multiple_clust.html`_ and corresponding script `load_multiple_clusterg
 
 Clustergrammer-JS API
 =====================
-Clustergrammer-JS' API allows users to pass options to the front-end visualization, such as optional callback functions.
+
+.. js:class:: Clustergrammer(args)
+
+  The Clusterrammer JavaScript object takes the ``args`` object and produces a visualization on the page.
+
+  This ``args`` object has two requried arguments, ``network_data`` and ``root``:
+
+    .. js:attribute:: args.network_data
+
+      This required attribute is where the visualization JSON should be passed as a JavaScript object.
+
+    .. js:attribute:: args.root
+
+      This required attribute is the ``id`` (passed as a string) of the container where Clustergrammer will be built. Each Clustergrammer visualization in a page should be passed a unique ``id``.
+
+    .. js:attribute:: args.about
+
+      This attribute is a string (which can include HTML) that will produce a small about section at the top of the sidebar. This can be used to provide a quick description about the data or visualization.
+
+    .. js:attribute:: args.row_tip_callback
+
+      Users can pass a callback function that will run when mousing over row labels.
+
+    .. js:attribute:: args.col_tip_callback
+
+      Users can pass a callback function that will run when mousing over col labels.
+
+    .. js:attribute:: args.tile_tip_callback
+
+      Users can pass a callback function that will run when mousing over a matrix-cell (e.g. matrix tile).
+
+    .. js:attribute:: args.dendro_callback
+
+      Users can pass a callback function that will run when mousing over a dendrogram cluster (e.g. gray trapezoid)
+
+    .. js:attribute:: args.matrix_update_callback
+
+      Users can pass a callback function that will run anytime the matrix has been updated, for instance when filtering/unfiltering, cropping, etc.
+
+    .. js:attribute:: args.sidebar_width:
+
+      Users can modify the width of the sidebar by specifying the width of the sidebar in pixels as a number.
+
+    .. js:attribute:: args.ini_view
+
+      Users can initialize the 'view' of their matrix, e.g. a initialize the matrix at a particular row filtering level.
+
+  Clustergrammer's attributes and functions are listed below:
+
+  .. js:function:: update_cats(row_data)
+
+    Update the visualization row categories.
+
+    :param row_data: The row category data that will be used to ...
+
+    :param resize_viz: Call this function to resize the visualization to fit in its resized container (if the user has resized the container).
+
+
 
 .. _visualization_json:
 

docs/_build_html/_sources/clustergrammer_py.rst.txt

@@ -55,13 +55,12 @@ Clustergrammer-PY generates a Network object (see `Network class definition`_),
 
 When a matrix is loaded into an instance of ``Network`` (e.g. ``net``) it is stored in the data, ``dat``, attribute. Normalization and filtering will modify the ``dat`` representation of the matrix. When the matrix is clustered (by calling :ref:`make_clust`)
 
-.. automodule:: clustergrammer
+.. automodule:: clustergrammer_py
 
 .. autoclass:: Network
     :members:
 
 
-
 .. _clustergrammer_py_dev:
 
 Clustergrammer-PY Development

docs/_build_html/_sources/clustergrammer_py.txt

@@ -53,15 +53,14 @@ Clustergrammer-PY API
 =====================
 Clustergrammer-PY generates a Network object (see `Network class definition`_), which is used to load a matrix (e.g. from a Pandas `DataFrame`_), optionally normalize or filter the matrix, cluster the matrix, and finally generate the visualization JSON for the front-end Clustergrammer.js.
 
-When a matrix is loaded into an instance of ``Network`` (e.g. ``net``) it is stored in the data, ``dat``, attribute. Normalization and filtering will modify the ``dat`` representation of the matrix. When the matrix is clustered (by calling the ``make_clust`` function)
+When a matrix is loaded into an instance of ``Network`` (e.g. ``net``) it is stored in the data, ``dat``, attribute. Normalization and filtering will modify the ``dat`` representation of the matrix. When the matrix is clustered (by calling :ref:`make_clust`)
 
 .. automodule:: clustergrammer_py
 
 .. autoclass:: Network
     :members:
 
 
-
 .. _clustergrammer_py_dev:
 
 Clustergrammer-PY Development

docs/_build_html/clustergrammer_js.html

@@ -190,7 +190,94 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 </div>
 <div class="section" id="clustergrammer-js-api">
 <span id="id4"></span><h2>Clustergrammer-JS API<a class="headerlink" href="#clustergrammer-js-api" title="Permalink to this headline">¶</a></h2>
-<p>Clustergrammer-JS&#8217; API allows users to pass options to the front-end visualization, such as optional callback functions.</p>
+<dl class="class">
+<dt id="Clustergrammer">
+<em class="property">class </em><code class="descname">Clustergrammer</code><span class="sig-paren">(</span><em>args</em><span class="sig-paren">)</span><a class="headerlink" href="#Clustergrammer" title="Permalink to this definition">¶</a></dt>
+<dd><p>The Clusterrammer JavaScript object takes the <code class="docutils literal"><span class="pre">args</span></code> object and produces a visualization on the page.</p>
+<p>This <code class="docutils literal"><span class="pre">args</span></code> object has two requried arguments, <code class="docutils literal"><span class="pre">network_data</span></code> and <code class="docutils literal"><span class="pre">root</span></code>:</p>
+<blockquote>
+<div><dl class="attribute">
+<dt id="args.network_data">
+<code class="descclassname">args.</code><code class="descname">network_data</code><a class="headerlink" href="#args.network_data" title="Permalink to this definition">¶</a></dt>
+<dd><p>This required attribute is where the visualization JSON should be passed as a JavaScript object.</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="args.root">
+<code class="descclassname">args.</code><code class="descname">root</code><a class="headerlink" href="#args.root" title="Permalink to this definition">¶</a></dt>
+<dd><p>This required attribute is the <code class="docutils literal"><span class="pre">id</span></code> (passed as a string) of the container where Clustergrammer will be built. Each Clustergrammer visualization in a page should be passed a unique <code class="docutils literal"><span class="pre">id</span></code>.</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="args.about">
+<code class="descclassname">args.</code><code class="descname">about</code><a class="headerlink" href="#args.about" title="Permalink to this definition">¶</a></dt>
+<dd><p>This attribute is a string (which can include HTML) that will produce a small about section at the top of the sidebar. This can be used to provide a quick description about the data or visualization.</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="args.row_tip_callback">
+<code class="descclassname">args.</code><code class="descname">row_tip_callback</code><a class="headerlink" href="#args.row_tip_callback" title="Permalink to this definition">¶</a></dt>
+<dd><p>Users can pass a callback function that will run when mousing over row labels.</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="args.col_tip_callback">
+<code class="descclassname">args.</code><code class="descname">col_tip_callback</code><a class="headerlink" href="#args.col_tip_callback" title="Permalink to this definition">¶</a></dt>
+<dd><p>Users can pass a callback function that will run when mousing over col labels.</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="args.tile_tip_callback">
+<code class="descclassname">args.</code><code class="descname">tile_tip_callback</code><a class="headerlink" href="#args.tile_tip_callback" title="Permalink to this definition">¶</a></dt>
+<dd><p>Users can pass a callback function that will run when mousing over a matrix-cell (e.g. matrix tile).</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="args.dendro_callback">
+<code class="descclassname">args.</code><code class="descname">dendro_callback</code><a class="headerlink" href="#args.dendro_callback" title="Permalink to this definition">¶</a></dt>
+<dd><p>Users can pass a callback function that will run when mousing over a dendrogram cluster (e.g. gray trapezoid)</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="args.matrix_update_callback">
+<code class="descclassname">args.</code><code class="descname">matrix_update_callback</code><a class="headerlink" href="#args.matrix_update_callback" title="Permalink to this definition">¶</a></dt>
+<dd><p>Users can pass a callback function that will run anytime the matrix has been updated, for instance when filtering/unfiltering, cropping, etc.</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="args.sidebar_width:">
+<code class="descclassname">args.</code><code class="descname">sidebar_width:</code><a class="headerlink" href="#args.sidebar_width:" title="Permalink to this definition">¶</a></dt>
+<dd><p>Users can modify the width of the sidebar by specifying the width of the sidebar in pixels as a number.</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="args.ini_view">
+<code class="descclassname">args.</code><code class="descname">ini_view</code><a class="headerlink" href="#args.ini_view" title="Permalink to this definition">¶</a></dt>
+<dd><p>Users can initialize the &#8216;view&#8217; of their matrix, e.g. a initialize the matrix at a particular row filtering level.</p>
+</dd></dl>
+
+</div></blockquote>
+<p>Clustergrammer&#8217;s attributes and functions are listed below:</p>
+<dl class="function">
+<dt id="update_cats">
+<code class="descname">update_cats</code><span class="sig-paren">(</span><em>row_data</em><span class="sig-paren">)</span><a class="headerlink" href="#update_cats" title="Permalink to this definition">¶</a></dt>
+<dd><p>Update the visualization row categories.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Arguments:</th><td class="field-body"><ul class="first last simple">
+<li><strong>row_data</strong> &#8211; The row category data that will be used to ...</li>
+<li><strong>resize_viz</strong> &#8211; Call this function to resize the visualization to fit in its resized container (if the user has resized the container).</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
 </div>
 <div class="section" id="visualization-json">
 <span id="id5"></span><h2>Visualization-JSON<a class="headerlink" href="#visualization-json" title="Permalink to this headline">¶</a></h2>

docs/_build_html/clustergrammer_py.html

@@ -191,7 +191,7 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 <div class="section" id="clustergrammer-py-api">
 <span id="id2"></span><h2>Clustergrammer-PY API<a class="headerlink" href="#clustergrammer-py-api" title="Permalink to this headline">¶</a></h2>
 <p>Clustergrammer-PY generates a Network object (see <a class="reference external" href="https://github.com/MaayanLab/clustergrammer-py/blob/master/clustergrammer/__init__.py">Network class definition</a>), which is used to load a matrix (e.g. from a Pandas <a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.html">DataFrame</a>), optionally normalize or filter the matrix, cluster the matrix, and finally generate the visualization JSON for the front-end Clustergrammer.js.</p>
-<p>When a matrix is loaded into an instance of <code class="docutils literal"><span class="pre">Network</span></code> (e.g. <code class="docutils literal"><span class="pre">net</span></code>) it is stored in the data, <code class="docutils literal"><span class="pre">dat</span></code>, attribute. Normalization and filtering will modify the <code class="docutils literal"><span class="pre">dat</span></code> representation of the matrix. When the matrix is clustered (by calling the <code class="docutils literal"><span class="pre">make_clust</span></code> function)</p>
+<p>When a matrix is loaded into an instance of <code class="docutils literal"><span class="pre">Network</span></code> (e.g. <code class="docutils literal"><span class="pre">net</span></code>) it is stored in the data, <code class="docutils literal"><span class="pre">dat</span></code>, attribute. Normalization and filtering will modify the <code class="docutils literal"><span class="pre">dat</span></code> representation of the matrix. When the matrix is clustered (by calling <span class="xref std std-ref">make_clust</span>)</p>
 <span class="target" id="module-clustergrammer_py"></span><dl class="class">
 <dt id="clustergrammer_py.Network">
 <em class="property">class </em><code class="descclassname">clustergrammer_py.</code><code class="descname">Network</code><a class="headerlink" href="#clustergrammer_py.Network" title="Permalink to this definition">¶</a></dt>

docs/_build_html/genindex.html

@@ -140,7 +140,8 @@
 <h1 id="index">Index</h1>
 
 <div class="genindex-jumpbox">
- <a href="#C"><strong>C</strong></a>
+ <a href="#A"><strong>A</strong></a>
+ | <a href="#C"><strong>C</strong></a>
  | <a href="#D"><strong>D</strong></a>
  | <a href="#E"><strong>E</strong></a>
  | <a href="#F"><strong>F</strong></a>
@@ -150,13 +151,68 @@ <h1 id="index">Index</h1>
  | <a href="#P"><strong>P</strong></a>
  | <a href="#R"><strong>R</strong></a>
  | <a href="#S"><strong>S</strong></a>
+ | <a href="#U"><strong>U</strong></a>
  | <a href="#W"><strong>W</strong></a>
 
 </div>
+<h2 id="A">A</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+
+  <dt><a href="clustergrammer_js.html#args.about">args.about (args attribute)</a>
+  </dt>
+
+
+  <dt><a href="clustergrammer_js.html#args.col_tip_callback">args.col_tip_callback (args attribute)</a>
+  </dt>
+
+
+  <dt><a href="clustergrammer_js.html#args.dendro_callback">args.dendro_callback (args attribute)</a>
+  </dt>
+
+
+  <dt><a href="clustergrammer_js.html#args.ini_view">args.ini_view (args attribute)</a>
+  </dt>
+
+
+  <dt><a href="clustergrammer_js.html#args.matrix_update_callback">args.matrix_update_callback (args attribute)</a>
+  </dt>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+
+  <dt><a href="clustergrammer_js.html#args.network_data">args.network_data (args attribute)</a>
+  </dt>
+
+
+  <dt><a href="clustergrammer_js.html#args.root">args.root (args attribute)</a>
+  </dt>
+
+
+  <dt><a href="clustergrammer_js.html#args.row_tip_callback">args.row_tip_callback (args attribute)</a>
+  </dt>
+
+
+  <dt><a href="clustergrammer_js.html#args.sidebar_width:">args.sidebar_width: (args attribute)</a>
+  </dt>
+
+
+  <dt><a href="clustergrammer_js.html#args.tile_tip_callback">args.tile_tip_callback (args attribute)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
 <h2 id="C">C</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
 
+  <dt><a href="clustergrammer_js.html#Clustergrammer">Clustergrammer() (class)</a>
+  </dt>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+
   <dt><a href="clustergrammer_py.html#module-clustergrammer_py">clustergrammer_py (module)</a>
   </dt>
 
@@ -307,6 +363,16 @@ <h2 id="S">S</h2>
   </dl></td>
 </tr></table>
 
+<h2 id="U">U</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+
+  <dt><a href="clustergrammer_js.html#update_cats">update_cats() (built-in function)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
 <h2 id="W">W</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>