working on homepage

docs/_build_html/_sources/clustergrammer_js.txt

@@ -87,4 +87,4 @@ Please :ref:`contact` Nicolas Fernandez or Avi Ma'ayan with questions or use the
 .. |npm-version| image:: https://img.shields.io/npm/v/clustergrammer.svg
     :alt: version
     :scale: 100%
-    :target: https://www.npmjs.com/package/clustergrammer
+    :target: https://www.npmjs.com/package/clustergrammer

docs/_build_html/_sources/clustergrammer_widget.txt

@@ -3,6 +3,7 @@
 Clustergrammer Jupyter Widget
 -----------------------------
 |pypi-version|
+|npm-version|
 
 Clustergrammer can be used within a Jupyter notebook as an interactive HTML widget and is compatable with Python 2 and 3. Clustergrammer-Widget can be used to visualize a matrix of data from a file or from a `Pandas`_ DataFrame.
 
@@ -72,6 +73,11 @@ Please :ref:`contact` Nicolas Fernandez or Avi Ma'ayan with questions or use the
 .. _`SciPy`: https://www.scipy.org/
 
 .. |pypi-version| image:: https://img.shields.io/pypi/v/clustergrammer_widget.svg
-    :alt: version
+    :alt: pypi-version
     :scale: 100%
-    :target: https://pypi.python.org/pypi?:action=display&name=clustergrammer_widget
+    :target: https://pypi.python.org/pypi?:action=display&name=clustergrammer_widget
+
+.. |npm-version| image:: https://img.shields.io/npm/v/clustergrammer_widget.svg
+    :alt: npm-version
+    :scale: 100%
+    :target: https://www.npmjs.com/package/clustergrammer_widget

docs/_build_html/_sources/index.txt

@@ -4,7 +4,7 @@ Welcome to Clustergrammer's Documentation!
 ------------------------------------------
 Clustergrammer is a web-based tool for visualizing high-dimensional data as interactive and shareable hierarchically clustered heatmaps. The front-end is built using D3.js and back-end calculations are done using Python. The easiest ways to use Clustergrammer are to:
 
-- upload a file with your data to the `Clustergrammer web application`_,
+- upload a file with your data to the Clustergrammer web application ``_,
 - or visualize your data within a Jupyter notebook using Clustergrammer-Widget.
 
 Please read the :doc:`getting_started` guide for more information.
@@ -21,9 +21,9 @@ About Clustergrammer
 ====================
 Clustergrammer is a web-based visualization tool for visualizing high-dimensional data (e.g. a matrix of data) using hierarchically clustered heatmaps. Clustergrammer's front-end (Clustergrammer.js) is built using D3.js and its back-end (Clustergrammer.py) is built using Python (e.g. SciPy). The Clustergrammer project is modular and can be used in several ways:
 
-#. :ref:`Web application <getting_started_web_app>`
-#. Jupyter Notebook :ref:`Interactive Widget <getting_started_widget>`
-#. `JavaScript <https://github.com/MaayanLab/clustergrammer>`_ and `Python <https://github.com/MaayanLab/clustergrammer-py>`_ Libraries
+#. :ref:`clustergrammer_web`
+#. :ref:`clustergrammer_widget`
+#. :ref:`clustergrammer_js` and :ref:`clustergrammer_py` libraries
 
 The web application is the easiest way for a user to generate an interactive and shareable visualization. For more technical users, the Jupyter widget enables visualizations to be built within Jupyter notebook workflows and shared through Jupyter's Nbviewer. Finally, web developers can use Clustergrammer's libraries or Clustergrammer-Web's API to dynamically generate visualizations for their own web appliications.
 
@@ -76,7 +76,7 @@ Contact
 Please contact Avi Ma'ayan (avi.maayan@mssm.edu) and Nicolas Fernandez (nicolas.fernandez@mssm.edu) for support, comments, and suggestions.
 
 
-.. _`Clustergrammer web application`: http://amp.pharm.mssm.edu/clustergrammer/
+.. _`homepage`: http://amp.pharm.mssm.edu/clustergrammer/
 .. _`Enrichr`: http://amp.pharm.mssm.edu/Enrichr/
 .. _`GEN3VA`: http://amp.pharm.mssm.edu/gen3va/
 .. _`L1000CDS2`: http://amp.pharm.mssm.edu/l1000cds2/

docs/_build_html/clustergrammer_js.html

@@ -32,7 +32,7 @@
 
     <link rel="top" title="Clustergrammer 1.0.0 documentation" href="index.html"/>
         <link rel="next" title="Clustergrammer-PY" href="clustergrammer_py.html"/>
-        <link rel="prev" title="Building a Webpage" href="building_webpage.html"/> 
+        <link rel="prev" title="Clustergrammer for Web-development" href="building_webpage.html"/> 
 
 
   <script src="_static/js/modernizr.min.js"></script>
@@ -83,13 +83,13 @@
 
                 <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">Clustergrammer Web App</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="clustergrammer_web.html">Clustergrammer Web App</a></li>
+<li class="toctree-l1"><a class="reference internal" href="clustergrammer_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>
 <li class="toctree-l1"><a class="reference internal" href="matrix_format_io.html">Matrix Formats and Input/Output</a></li>
-<li class="toctree-l1"><a class="reference internal" href="building_webpage.html">Building a Webpage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="building_webpage.html">Clustergrammer for Web-development</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Clustergrammer-JS</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#dependencies">Dependencies</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#installation">Installation</a></li>
@@ -196,7 +196,7 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 </div>
 <div class="section" id="clustergrammer-js-development">
 <span id="clustergrammer-js-dev"></span><h2>Clustergrammer-JS Development<a class="headerlink" href="#clustergrammer-js-development" 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 App</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&#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="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web App</span></a> and the <a class="reference internal" href="clustergrammer_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>.</p>
 <p>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>
@@ -212,7 +212,7 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
         <a href="clustergrammer_py.html" class="btn btn-neutral float-right" title="Clustergrammer-PY" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
-        <a href="building_webpage.html" class="btn btn-neutral" title="Building a Webpage" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+        <a href="building_webpage.html" class="btn btn-neutral" title="Clustergrammer for Web-development" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
 
     </div>
 

docs/_build_html/clustergrammer_widget.html

@@ -146,7 +146,8 @@
 
   <div class="section" id="clustergrammer-jupyter-widget">
 <span id="clustergrammer-widget"></span><h1>Clustergrammer Jupyter Widget<a class="headerlink" href="#clustergrammer-jupyter-widget" title="Permalink to this headline">¶</a></h1>
-<p><a class="reference external" href="https://pypi.python.org/pypi?:action=display&amp;name=clustergrammer_widget"><img alt="version" src="https://img.shields.io/pypi/v/clustergrammer_widget.svg" /></a></p>
+<p><a class="reference external" href="https://pypi.python.org/pypi?:action=display&amp;name=clustergrammer_widget"><img alt="pypi-version" src="https://img.shields.io/pypi/v/clustergrammer_widget.svg" /></a>
+<a class="reference external" href="https://www.npmjs.com/package/clustergrammer_widget"><img alt="npm-version" src="https://img.shields.io/npm/v/clustergrammer_widget.svg" /></a></p>
 <p>Clustergrammer can be used within a Jupyter notebook as an interactive HTML widget and is compatable with Python 2 and 3. Clustergrammer-Widget can be used to visualize a matrix of data from a file or from a <a class="reference external" href="http://pandas.pydata.org/">Pandas</a> DataFrame.</p>
 <div class="section" id="dependencies">
 <h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>

docs/_build_html/getting_started.html

@@ -31,7 +31,7 @@
 
 
     <link rel="top" title="Clustergrammer 1.0.0 documentation" href="index.html"/>
-        <link rel="next" title="Clustergrammer Web App" href="web_app.html"/>
+        <link rel="next" title="Clustergrammer Web App" href="clustergrammer_web.html"/>
         <link rel="prev" title="Welcome to Clustergrammer’s Documentation!" href="index.html"/> 
 
 
@@ -89,13 +89,13 @@
 <li class="toctree-l2"><a class="reference internal" href="#interacting-with-clustergrammer">Interacting with Clustergrammer</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="web_app.html">Clustergrammer Web App</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="clustergrammer_web.html">Clustergrammer Web App</a></li>
+<li class="toctree-l1"><a class="reference internal" href="clustergrammer_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>
 <li class="toctree-l1"><a class="reference internal" href="matrix_format_io.html">Matrix Formats and Input/Output</a></li>
-<li class="toctree-l1"><a class="reference internal" href="building_webpage.html">Building a Webpage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="building_webpage.html">Clustergrammer for Web-development</a></li>
 <li class="toctree-l1"><a class="reference internal" href="clustergrammer_js.html">Clustergrammer-JS</a></li>
 <li class="toctree-l1"><a class="reference internal" href="clustergrammer_py.html">Clustergrammer-PY</a></li>
 <li class="toctree-l1"><a class="reference internal" href="developing_with_clustergrammer.html">Developing Clustergrammer</a></li>
@@ -150,11 +150,11 @@ <h1>Getting Started<a class="headerlink" href="#getting-started" title="Permalin
 <h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
 <p>Clustergrammer is a web-based tool for visualizing high-dimensional data as interactive and shareable hierarchically clustered heatmaps. Clustergrammer can be used in three main ways:</p>
 <ol class="arabic simple">
-<li><a class="reference internal" href="web_app.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web App</span></a></li>
-<li><a class="reference internal" href="jupyter_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer Jupyter Widget</span></a></li>
+<li><a class="reference internal" href="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web App</span></a></li>
+<li><a class="reference internal" href="clustergrammer_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer Jupyter Widget</span></a></li>
 <li><a class="reference internal" href="clustergrammer_js.html#clustergrammer-js"><span class="std std-ref">Clustergrammer-JS</span></a> and <a class="reference internal" href="clustergrammer_py.html#clustergrammer-py"><span class="std std-ref">Clustergrammer-PY</span></a> libraries</li>
 </ol>
-<p>This section will provide instructions on how to quickly generate a visualization from a matrix of data using the <a class="reference internal" href="web_app.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web App</span></a> and the <a class="reference internal" href="jupyter_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer Jupyter Widget</span></a> as well as instructions on how to interact with the visualization. For developers interested in building their own web page using Clustergrammer, please see the <a class="reference internal" href="building_webpage.html#building-web-page"><span class="std std-ref">Building a Webpage</span></a> section.</p>
+<p>This section will provide instructions on how to quickly generate a visualization from a matrix of data using the <a class="reference internal" href="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web App</span></a> and the <a class="reference internal" href="clustergrammer_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer Jupyter Widget</span></a> as well as instructions on how to interact with the visualization. For developers interested in building their own web page using Clustergrammer, please see the <a class="reference internal" href="building_webpage.html#building-web-page"><span class="std std-ref">Clustergrammer for Web-development</span></a> section.</p>
 </div>
 <div class="section" id="clustergrammer-web">
 <span id="getting-started-web-app"></span><h2>Clustergrammer-Web<a class="headerlink" href="#clustergrammer-web" title="Permalink to this headline">¶</a></h2>
@@ -193,7 +193,7 @@ <h2>Interacting with Clustergrammer<a class="headerlink" href="#interacting-with
 
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
-        <a href="web_app.html" class="btn btn-neutral float-right" title="Clustergrammer Web App" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+        <a href="clustergrammer_web.html" class="btn btn-neutral float-right" title="Clustergrammer Web App" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
         <a href="index.html" class="btn btn-neutral" title="Welcome to Clustergrammer’s Documentation!" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>

docs/_build_html/index.html

@@ -141,7 +141,7 @@
 <h1>Welcome to Clustergrammer&#8217;s Documentation!<a class="headerlink" href="#welcome-to-clustergrammer-s-documentation" title="Permalink to this headline">¶</a></h1>
 <p>Clustergrammer is a web-based tool for visualizing high-dimensional data as interactive and shareable hierarchically clustered heatmaps. The front-end is built using D3.js and back-end calculations are done using Python. The easiest ways to use Clustergrammer are to:</p>
 <ul class="simple">
-<li>upload a file with your data to the <a class="reference external" href="http://amp.pharm.mssm.edu/clustergrammer/">Clustergrammer web application</a>,</li>
+<li>upload a file with your data to the Clustergrammer web application <a href="#id1"><span class="problematic" id="id2">``</span></a>_,</li>
 <li>or visualize your data within a Jupyter notebook using Clustergrammer-Widget.</li>
 </ul>
 <p>Please read the <a class="reference internal" href="getting_started.html"><span class="doc">Getting Started</span></a> guide for more information.</p>
@@ -153,9 +153,9 @@ <h2>Interactive Demo<a class="headerlink" href="#interactive-demo" title="Permal
 <h2>About Clustergrammer<a class="headerlink" href="#about-clustergrammer" title="Permalink to this headline">¶</a></h2>
 <p>Clustergrammer is a web-based visualization tool for visualizing high-dimensional data (e.g. a matrix of data) using hierarchically clustered heatmaps. Clustergrammer&#8217;s front-end (Clustergrammer.js) is built using D3.js and its back-end (Clustergrammer.py) is built using Python (e.g. SciPy). The Clustergrammer project is modular and can be used in several ways:</p>
 <ol class="arabic simple">
-<li><a class="reference internal" href="getting_started.html#getting-started-web-app"><span class="std std-ref">Web application</span></a></li>
-<li>Jupyter Notebook <a class="reference internal" href="getting_started.html#getting-started-widget"><span class="std std-ref">Interactive Widget</span></a></li>
-<li><a class="reference external" href="https://github.com/MaayanLab/clustergrammer">JavaScript</a> and <a class="reference external" href="https://github.com/MaayanLab/clustergrammer-py">Python</a> Libraries</li>
+<li><a class="reference internal" href="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web App</span></a></li>
+<li><a class="reference internal" href="clustergrammer_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer Jupyter Widget</span></a></li>
+<li><a class="reference internal" href="clustergrammer_js.html#clustergrammer-js"><span class="std std-ref">Clustergrammer-JS</span></a> and <a class="reference internal" href="clustergrammer_py.html#clustergrammer-py"><span class="std std-ref">Clustergrammer-PY</span></a> libraries</li>
 </ol>
 <p>The web application is the easiest way for a user to generate an interactive and shareable visualization. For more technical users, the Jupyter widget enables visualizations to be built within Jupyter notebook workflows and shared through Jupyter&#8217;s Nbviewer. Finally, web developers can use Clustergrammer&#8217;s libraries or Clustergrammer-Web&#8217;s API to dynamically generate visualizations for their own web appliications.</p>
 </div>
@@ -252,7 +252,7 @@ <h2>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Pe
 </ul>
 </div>
 <div class="section" id="contact">
-<span id="id1"></span><h2>Contact<a class="headerlink" href="#contact" title="Permalink to this headline">¶</a></h2>
+<span id="id3"></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>

docs/clustergrammer_js.rst

@@ -87,4 +87,4 @@ Please :ref:`contact` Nicolas Fernandez or Avi Ma'ayan with questions or use the
 .. |npm-version| image:: https://img.shields.io/npm/v/clustergrammer.svg
     :alt: version
     :scale: 100%
-    :target: https://www.npmjs.com/package/clustergrammer
+    :target: https://www.npmjs.com/package/clustergrammer