cleaning up contents titles

docs/_build_html/_sources/app_integration.rst.txt

@@ -1,7 +1,7 @@
 .. _app_integration:
 
-App Integration Examples
-------------------------
+App Integrations
+----------------
 Clustergrammer can be integrated into web applications to dynamically produce interactive visualizations -- see :ref:`building_web_page` for information. Clustergrammer is currently being utilized to visualize data for the following `Ma'ayan lab`_ web applications:
 
 Enrichr

docs/_build_html/_sources/building_webpage.rst.txt

@@ -1,7 +1,7 @@
 .. _building_web_page:
 
-Web-Development with Clustergrammer
------------------------------------
+Web-Development
+---------------
 Clustergrammer can be used by developers to add interactive heatmap visualizations to their web pages and web applications (see :ref:`app_integration`).
 
 Embedding Clustergrammer

docs/_build_html/_sources/developing_with_clustergrammer.rst.txt

@@ -1,5 +1,5 @@
-Developing Clustergrammer
--------------------------
+Developing
+----------
 Developers interested in working with the source code or in contributing to the Clustergrammer project can find instructions for the sub-projects here:
 
 #. :ref:`clustergrammer_js_dev`

docs/_build_html/app_integration.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>App Integration Examples &mdash; Clustergrammer 1.1.0 documentation</title>
+  <title>App Integrations &mdash; Clustergrammer 1.1.0 documentation</title>
 
 
 
@@ -29,7 +29,7 @@
   <link rel="stylesheet" href="https://unpkg.com/font-awesome@4.5.0/css/font-awesome.min.css" type="text/css" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="Developing Clustergrammer" href="developing_with_clustergrammer.html" />
+    <link rel="next" title="Developing" href="developing_with_clustergrammer.html" />
     <link rel="prev" title="Clustergrammer-PY" href="clustergrammer_py.html" /> 
 
 
@@ -85,24 +85,25 @@
 
               <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="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="case_studies.html">Case Studies and Tutorials</a></li>
+<li class="toctree-l1"><a class="reference internal" href="clustergrammer_web.html">Clustergrammer-Web</a></li>
+<li class="toctree-l1"><a class="reference internal" href="clustergrammer2.html">Clustergrammer2 Widget</a></li>
 <li class="toctree-l1"><a class="reference internal" href="interacting_with_viz.html">Interacting with the 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 and Examples</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">Web-Development with Clustergrammer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="building_webpage.html">Web-Development</a></li>
+<li class="toctree-l1"><a class="reference internal" href="clustergrammer_widget.html">Clustergrammer-Widget</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_gl.html">Clustergrammer-GL</a></li>
 <li class="toctree-l1"><a class="reference internal" href="clustergrammer_py.html">Clustergrammer-PY</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">App Integration Examples</a><ul>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">App Integrations</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#enrichr">Enrichr</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#gen3va">GEN3VA</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#l1000cds2">L1000CDS2</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#harmonizome">Harmonizome</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="developing_with_clustergrammer.html">Developing Clustergrammer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="developing_with_clustergrammer.html">Developing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
 </ul>
 
@@ -149,7 +150,7 @@
 
       <li><a href="index.html">Docs</a> &raquo;</li>
 
-      <li>App Integration Examples</li>
+      <li>App Integrations</li>
 
 
       <li class="wy-breadcrumbs-aside">
@@ -168,15 +169,15 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <div class="section" id="app-integration-examples">
-<span id="app-integration"></span><h1>App Integration Examples<a class="headerlink" href="#app-integration-examples" title="Permalink to this headline">¶</a></h1>
-<p>Clustergrammer can be integrated into web applications to dynamically produce interactive visualizations – see <a class="reference internal" href="building_webpage.html#building-web-page"><span class="std std-ref">Web-Development with Clustergrammer</span></a> for information. Clustergrammer is currently being utilized to visualize data for the following <a class="reference external" href="http://labs.icahn.mssm.edu/maayanlab/">Ma’ayan lab</a> web applications:</p>
+  <div class="section" id="app-integrations">
+<span id="app-integration"></span><h1>App Integrations<a class="headerlink" href="#app-integrations" title="Permalink to this headline">¶</a></h1>
+<p>Clustergrammer can be integrated into web applications to dynamically produce interactive visualizations – see <a class="reference internal" href="building_webpage.html#building-web-page"><span class="std std-ref">Web-Development</span></a> for information. Clustergrammer is currently being utilized to visualize data for the following <a class="reference external" href="http://labs.icahn.mssm.edu/maayanlab/">Ma’ayan lab</a> web applications:</p>
 <div class="section" id="enrichr">
 <h2>Enrichr<a class="headerlink" href="#enrichr" title="Permalink to this headline">¶</a></h2>
 <p>The enrichment analysis tool, <a class="reference external" href="http://amp.pharm.mssm.edu/Enrichr/">Enrichr</a>, uses Clustergrammer to produce dynamic heatmaps of enriched terms as columns and user input genes as rows, which helps users understand the relationships between their input genes and enriched terms.</p>
 <div class="figure align-left" id="id5">
 <a class="reference external image-reference" href="http://amp.pharm.mssm.edu/Enrichr/"><img alt="Enirchr Clustergram" src="_images/enrichr_screenshot_logo.png" style="width: 550px;" /></a>
-<p class="caption"><span class="caption-text"><a class="reference external" href="http://amp.pharm.mssm.edu/Enrichr/">Enrichr</a> uses the <a class="reference internal" href="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web App</span></a> API to produce interactive heatmaps of enriched terms as columns and user-input genes as rows.</span></p>
+<p class="caption"><span class="caption-text"><a class="reference external" href="http://amp.pharm.mssm.edu/Enrichr/">Enrichr</a> uses the <a class="reference internal" href="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer-Web</span></a> API to produce interactive heatmaps of enriched terms as columns and user-input genes as rows.</span></p>
 </div>
 </div>
 <div class="section" id="gen3va">
@@ -189,15 +190,15 @@ <h2>GEN3VA<a class="headerlink" href="#gen3va" title="Permalink to this headline
 </div>
 <div class="section" id="l1000cds2">
 <h2>L1000CDS2<a class="headerlink" href="#l1000cds2" title="Permalink to this headline">¶</a></h2>
-<p><a class="reference external" href="http://amp.pharm.mssm.edu/l1000cds2/">L1000CDS2</a> uses the <a class="reference internal" href="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web App</span></a> API to produce interactive heatmaps of perturbagen gene signatures that mimic or reverse an input gene signature. This can be useful for users who are interested in the specific genes that are differentially regulated by the identified perturbagens.</p>
+<p><a class="reference external" href="http://amp.pharm.mssm.edu/l1000cds2/">L1000CDS2</a> uses the <a class="reference internal" href="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer-Web</span></a> API to produce interactive heatmaps of perturbagen gene signatures that mimic or reverse an input gene signature. This can be useful for users who are interested in the specific genes that are differentially regulated by the identified perturbagens.</p>
 <div class="figure align-left" id="id7">
 <a class="reference external image-reference" href="http://amp.pharm.mssm.edu/clustergrammer/l1000cds2/55e0b68a5bf3665f1a726bfa"><img alt="L1000CDS2 Clustergram" src="_images/l1000cds2_screenshot.png" style="width: 800px;" /></a>
 <p class="caption"><span class="caption-text"><a class="reference external" href="http://amp.pharm.mssm.edu/l1000cds2/">L1000CDS2</a> uses Clustergrammer to produce interactive visualizations of input gene signatures and perturbation signatures that mimick or reverse the user’s user-input signature. A users’s input signature is shown as rows with gene expression levels shown as row-bars (red/blue for up/down expression) and perturbations found to mimic/reverse their signature are shown as columns in the heatmap.</span></p>
 </div>
 </div>
 <div class="section" id="harmonizome">
 <h2>Harmonizome<a class="headerlink" href="#harmonizome" title="Permalink to this headline">¶</a></h2>
-<p>The <a class="reference external" href="http://amp.pharm.mssm.edu/Harmonizome/">Harmonizome</a> uses the <a class="reference internal" href="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web App</span></a> API to generate visualizations of curated biological datasets as heatmaps and adjacency matrices (e.g. to depict networks). The Harmonizome also uses the Clustergrammer to visualize the amount of biological information that is available for different families of genes in the <a class="reference external" href="http://amp.pharm.mssm.edu/harmonogram/">Harmonogram</a></p>
+<p>The <a class="reference external" href="http://amp.pharm.mssm.edu/Harmonizome/">Harmonizome</a> uses the <a class="reference internal" href="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer-Web</span></a> API to generate visualizations of curated biological datasets as heatmaps and adjacency matrices (e.g. to depict networks). The Harmonizome also uses the Clustergrammer to visualize the amount of biological information that is available for different families of genes in the <a class="reference external" href="http://amp.pharm.mssm.edu/harmonogram/">Harmonogram</a></p>
 <div class="figure align-left" id="id8">
 <a class="reference external image-reference" href="http://amp.pharm.mssm.edu/Harmonizome/visualize/heat_map/attribute_similarity"><img alt="Harmonizome Similarity Heatmap" src="_images/hzome_sim_mat.png" style="width: 800px;" /></a>
 <p class="caption"><span class="caption-text">The <a class="reference external" href="http://amp.pharm.mssm.edu/Harmonizome/">Harmonizome</a> uses Clustergrammer to visualize datasets as heatmaps and similarity matrices (e.g. similarity of attributes based on shared genes). Above is an example similarity matrix of KEGG pathways.</span></p>
@@ -213,7 +214,7 @@ <h2>Harmonizome<a class="headerlink" href="#harmonizome" title="Permalink to thi
 
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
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+        <a href="developing_with_clustergrammer.html" class="btn btn-neutral float-right" title="Developing" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
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