clustergrammer_js.rst improvements

docs/_build_html/_sources/clustergrammer_js.txt

@@ -2,15 +2,15 @@
 
 Clustergrammer-JS
 -----------------
-Clustergrammer-JS is the front-end JavaScript library that builds the interactive heatmap visualization in SVG using the visualization library `D3.js`_
+Clustergrammer-JS is the front-end JavaScript library that builds the interactive heatmap visualization in `SVG`_ using the visualization library `D3.js`_
 
 
 Dependencies
 ============
 
-- D3.js
-- JQuery
-- Underscore
+- `D3.js`_
+- `JQuery`_
+- `Underscore`_
 
 Installation
 ============
@@ -19,7 +19,7 @@ Clustergrammer.js can be installed using node package manager (`npm package`_) w
 
   npm install clustergrammer
 
-or the source code can be obtained from the `Clustergrammer.js repo`_.
+or the source code and library, ``clustergrammer.js``, can be obtained from the `clustergrammer`_ Github repo.
 
 .. _javascript_workflow_example:
 
@@ -56,11 +56,20 @@ The JSON format required for Clustergrammer.js is described here:
 
 Open Source Code
 ================
+Clustergrammer-JS' source code can be found in the `clustergrammer`_ GihHub repo. The Clustergrammer-JS library is utilized by the :ref:`clustergrammer_web` and the :ref:`clustergrammer_widget`.
 
-.. _`Clustergrammer.js repo`: https://github.com/MaayanLab/clustergrammer
+Clustergrammer-JS is built with `Webpack Module Bundler`_ from the source files in `src`_. Please :ref:`contact` Nicolas Fernandez or Avi Ma'ayan with questions or use the GitHub `issues`_ feature to raise an issue.
+
+.. _`SVG`: https://en.wikipedia.org/wiki/Scalable_Vector_Graphics
+.. _`clustergrammer`: https://github.com/MaayanLab/clustergrammer
 .. _`npm package`: https://www.npmjs.com/package/clustergrammer
 .. _`index.html`: https://github.com/MaayanLab/clustergrammer/blob/master/index.html
 .. _`load_clustergram.js`: https://github.com/MaayanLab/clustergrammer/blob/master/js/load_clustergram.js
 .. _`multiple_clust.html`: https://github.com/MaayanLab/clustergrammer/blob/master/multiple_clustergrams.html
 .. _`load_multiple_clustergrams.js`: https://github.com/MaayanLab/clustergrammer/blob/master/js/load_multiple_clustergrams.js
-.. _`D3.js`: https://d3js.org/
+.. _`D3.js`: https://d3js.org/
+.. _`JQuery`: https://jquery.com/
+.. _`Underscore`: http://underscorejs.org/
+.. _`Webpack Module Bundler`: https://webpack.github.io/
+.. _`src`: https://github.com/MaayanLab/clustergrammer/tree/master/src
+.. _`issues`: https://github.com/MaayanLab/clustergrammer/issues

docs/_build_html/_sources/clustergrammer_py.txt

@@ -49,7 +49,7 @@ Clustergrammer-PY generates a Network object, which is used to load a matrix (e.
 
 Developing Clustergrammer-PY
 =============================
-Clustergrammer-PY's source code can be found in the `clustergrammer-py`_ Github repo. The Clustergrammer-PY library is utilized by the :ref:`clustergrammer_web` and the :ref:`clustergrammer_widget`.
+Clustergrammer-PY's source code can be found in the `clustergrammer-py`_ GitHub repo. The Clustergrammer-PY library is utilized by the :ref:`clustergrammer_web` and the :ref:`clustergrammer_widget`.
 
 .. _`GitHub repo`: http://github.com/MaayanLab/clustergrammer-py
 .. _`package index`: https://pypi.python.org/pypi?:action=display&name=clustergrammer

docs/_build_html/_sources/index.txt

@@ -68,6 +68,8 @@ Indices and tables
 * :ref:`genindex`
 * :ref:`search`
 
+.. _contact:
+
 Contact
 =======
 Please contact Avi Ma'ayan (avi.maayan@mssm.edu) and Nicolas Fernandez (nicolas.fernandez@mssm.edu) for support, comments, and suggestions.

docs/_build_html/clustergrammer_js.html

@@ -83,8 +83,8 @@
 
                 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="web_app.html">Web Application</a></li>
-<li class="toctree-l1"><a class="reference internal" href="jupyter_widget.html">Jupyter Widget</a></li>
+<li class="toctree-l1"><a class="reference internal" href="web_app.html">Clustergrammer Web Application</a></li>
+<li class="toctree-l1"><a class="reference internal" href="jupyter_widget.html">Clustergrammer Jupyter Widget</a></li>
 <li class="toctree-l1"><a class="reference internal" href="viz_interaction.html">Interactive Visualization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="biology_specific_features.html">Biology Specific Features</a></li>
 <li class="toctree-l1"><a class="reference internal" href="case_studies.html">Case Studies</a></li>
@@ -148,13 +148,13 @@
 
   <div class="section" id="clustergrammer-js">
 <span id="id1"></span><h1>Clustergrammer-JS<a class="headerlink" href="#clustergrammer-js" title="Permalink to this headline">¶</a></h1>
-<p>Clustergrammer-JS is the front-end JavaScript library that builds the interactive heatmap visualization in SVG using the visualization library <a class="reference external" href="https://d3js.org/">D3.js</a></p>
+<p>Clustergrammer-JS is the front-end JavaScript library that builds the interactive heatmap visualization in <a class="reference external" href="https://en.wikipedia.org/wiki/Scalable_Vector_Graphics">SVG</a> using the visualization library <a class="reference external" href="https://d3js.org/">D3.js</a></p>
 <div class="section" id="dependencies">
 <h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>
 <ul class="simple">
-<li>D3.js</li>
-<li>JQuery</li>
-<li>Underscore</li>
+<li><a class="reference external" href="https://d3js.org/">D3.js</a></li>
+<li><a class="reference external" href="https://jquery.com/">JQuery</a></li>
+<li><a class="reference external" href="http://underscorejs.org/">Underscore</a></li>
 </ul>
 </div>
 <div class="section" id="installation">
@@ -163,7 +163,7 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">npm</span> <span class="n">install</span> <span class="n">clustergrammer</span>
 </pre></div>
 </div>
-<p>or the source code can be obtained from the <a class="reference external" href="https://github.com/MaayanLab/clustergrammer">Clustergrammer.js repo</a>.</p>
+<p>or the source code and library, <code class="docutils literal"><span class="pre">clustergrammer.js</span></code>, can be obtained from the <a class="reference external" href="https://github.com/MaayanLab/clustergrammer">clustergrammer</a> Github repo.</p>
 </div>
 <div class="section" id="javascript-workflow-example">
 <span id="id2"></span><h2>JavaScript Workflow Example<a class="headerlink" href="#javascript-workflow-example" title="Permalink to this headline">¶</a></h2>
@@ -181,7 +181,7 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 </div>
 <div class="section" id="example-pages">
 <span id="id3"></span><h2>Example Pages<a class="headerlink" href="#example-pages" title="Permalink to this headline">¶</a></h2>
-<p>The <a class="reference external" href="https://github.com/MaayanLab/clustergrammer">Clustergrammer.js repo</a> contains several example pages demonstrating how to make a webpage with a Clustergramemr heatmap. The page <a class="reference external" href="https://github.com/MaayanLab/clustergrammer/blob/master/index.html">index.html</a> and corresponding script <a class="reference external" href="https://github.com/MaayanLab/clustergrammer/blob/master/js/load_clustergram.js">load_clustergram.js</a> show how to make a full-screen resizable visualization.</p>
+<p>The <a href="#id4"><span class="problematic" id="id5">`Clustergrammer.js repo`_</span></a> contains several example pages demonstrating how to make a webpage with a Clustergramemr heatmap. The page <a class="reference external" href="https://github.com/MaayanLab/clustergrammer/blob/master/index.html">index.html</a> and corresponding script <a class="reference external" href="https://github.com/MaayanLab/clustergrammer/blob/master/js/load_clustergram.js">load_clustergram.js</a> show how to make a full-screen resizable visualization.</p>
 <p>The page <a class="reference external" href="https://github.com/MaayanLab/clustergrammer/blob/master/multiple_clustergrams.html">multiple_clust.html</a> and corresponding script <a class="reference external" href="https://github.com/MaayanLab/clustergrammer/blob/master/js/load_multiple_clustergrams.js">load_multiple_clustergrams.js</a> show how to visualize multiple clustergrams on one page. Note that each heatmap requires its own container.</p>
 </div>
 <div class="section" id="clustergrammer-js-api">
@@ -194,6 +194,8 @@ <h2>Clustergrammer.js JSON Format<a class="headerlink" href="#clustergrammer-js-
 </div>
 <div class="section" id="open-source-code">
 <h2>Open Source Code<a class="headerlink" href="#open-source-code" title="Permalink to this headline">¶</a></h2>
+<p>Clustergrammer-JS&#8217; source code can be found in the <a class="reference external" href="https://github.com/MaayanLab/clustergrammer">clustergrammer</a> GihHub repo. The Clustergrammer-JS library is utilized by the <a class="reference internal" href="web_app.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web Application</span></a> and the <a class="reference internal" href="jupyter_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer Jupyter Widget</span></a>.</p>
+<p>Clustergrammer-JS is built with <a class="reference external" href="https://webpack.github.io/">Webpack Module Bundler</a> from the source files in <a class="reference external" href="https://github.com/MaayanLab/clustergrammer/tree/master/src">src</a>. Please <a class="reference internal" href="index.html#contact"><span class="std std-ref">Contact</span></a> Nicolas Fernandez or Avi Ma&#8217;ayan with questions or use the GitHub <a class="reference external" href="https://github.com/MaayanLab/clustergrammer/issues">issues</a> feature to raise an issue.</p>
 </div>
 </div>
 

docs/_build_html/clustergrammer_py.html

@@ -188,7 +188,7 @@ <h2>Clustergrammer-PY API<a class="headerlink" href="#clustergrammer-py-api" tit
 </div>
 <div class="section" id="developing-clustergrammer-py">
 <h2>Developing Clustergrammer-PY<a class="headerlink" href="#developing-clustergrammer-py" title="Permalink to this headline">¶</a></h2>
-<p>Clustergrammer-PY&#8217;s source code can be found in the <a class="reference external" href="https://github.com/MaayanLab/clustergrammer-py">clustergrammer-py</a> Github repo. The Clustergrammer-PY library is utilized by the <a class="reference internal" href="web_app.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web Application</span></a> and the <a class="reference internal" href="jupyter_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer Jupyter Widget</span></a>.</p>
+<p>Clustergrammer-PY&#8217;s source code can be found in the <a class="reference external" href="https://github.com/MaayanLab/clustergrammer-py">clustergrammer-py</a> GitHub repo. The Clustergrammer-PY library is utilized by the <a class="reference internal" href="web_app.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web Application</span></a> and the <a class="reference internal" href="jupyter_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer Jupyter Widget</span></a>.</p>
 </div>
 </div>
 

docs/_build_html/index.html

@@ -247,7 +247,7 @@ <h2>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Pe
 </ul>
 </div>
 <div class="section" id="contact">
-<h2>Contact<a class="headerlink" href="#contact" title="Permalink to this headline">¶</a></h2>
+<span id="id1"></span><h2>Contact<a class="headerlink" href="#contact" title="Permalink to this headline">¶</a></h2>
 <p>Please contact Avi Ma&#8217;ayan (<a class="reference external" href="mailto:avi&#46;maayan&#37;&#52;&#48;mssm&#46;edu">avi<span>&#46;</span>maayan<span>&#64;</span>mssm<span>&#46;</span>edu</a>) and Nicolas Fernandez (<a class="reference external" href="mailto:nicolas&#46;fernandez&#37;&#52;&#48;mssm&#46;edu">nicolas<span>&#46;</span>fernandez<span>&#64;</span>mssm<span>&#46;</span>edu</a>) for support, comments, and suggestions.</p>
 </div>
 </div>