app_integration dos

cornhundred · Feb 16, 2017 · 2cfc608 · 2cfc608
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diff --git a/docs/_build_html/.doctrees/app_integration.doctree b/docs/_build_html/.doctrees/app_integration.doctree
diff --git a/docs/_build_html/.doctrees/clustergrammer_js.doctree b/docs/_build_html/.doctrees/clustergrammer_js.doctree
diff --git a/docs/_build_html/.doctrees/environment.pickle b/docs/_build_html/.doctrees/environment.pickle
diff --git a/docs/_build_html/.doctrees/index.doctree b/docs/_build_html/.doctrees/index.doctree
diff --git a/docs/_build_html/_sources/app_integration.txt b/docs/_build_html/_sources/app_integration.txt
@@ -1,17 +1,31 @@
 .. _app_integration:
 
-Clustergrammer App Integrations
---------------------------------
-Clustergrammer can be integrated into other web applications and is being utilized to visualize data for the following Ma'ayan lab web applications:
+App Integration Examples
+------------------------
+Clustergrammer can be integrated into other web applications and is being utilized to visualize data for the following `Ma'ayan lab`_ web applications:
 
-- `Enrichr`_
-- `GEN3VA`_
-- `L1000CDS2`_
-- `GEO2Enrichr`_
-- `Harmonizome`_
+Enrichr
+=======
+The enrichment analysis tool, `Enrichr`_, uses the :ref:`clustergrammer_web`'s API to produce dynamic heatmaps of enriched terms as columns and user lists as rows. This helps users understand the relationships between their input genes and the returned enriched terms.
+
+GEN3VA
+======
+The gene signature analysis and visualization tool, `GEN3VA`_, uses Clustergrammer's core libraries, :ref:`clustergrammer_js` and :ref:`clustergrammer_py`, to dynamcally visualize collections of gene expression signatures collected by users from `GEO`_ as interactive heatmaps. GEN3VA also uses Clustergrammer to visualize enrichment analysis results (obtained from `Enrichr`_) and perturbations that reverse or mimic gene expression signatures (obtained from `L1000CDS2`_)
+
+L1000CDS2
+=========
+`L1000CDS2`_ uses the :ref:`clustergrammer_web`'s API to produce interactive heatmaps of perturbagen gene signatures that mimic or reverse an input gene signature. This can be useful for users that are interested in the specific genes that are differentially regulated by the identified perturbagens.
+
+Harmonizome
+===========
+The `Harmonizome`_ uses :ref:`clustergrammer_web`'s API to generate visualize of curated biological datasets as heatmaps and adjacency matrices (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 `Harmonogram`_
 
 .. _`Enrichr`: http://amp.pharm.mssm.edu/Enrichr/
 .. _`GEN3VA`: http://amp.pharm.mssm.edu/gen3va/
 .. _`L1000CDS2`: http://amp.pharm.mssm.edu/l1000cds2/
 .. _`GEO2Enrichr`: http://amp.pharm.mssm.edu/g2e/
-.. _`Harmonizome`: http://amp.pharm.mssm.edu/Harmonizome/
+.. _`Harmonizome`: http://amp.pharm.mssm.edu/Harmonizome/
+.. _`GEO`: https://www.ncbi.nlm.nih.gov/geo/
+.. _`L1000CDS2': http://amp.pharm.mssm.edu/l1000cds2/#/index
+.. _`Harmonogram`: http://amp.pharm.mssm.edu/harmonogram/
+.. _`Ma'ayan lab`: http://labs.icahn.mssm.edu/maayanlab/
diff --git a/docs/_build_html/_sources/clustergrammer_js.txt b/docs/_build_html/_sources/clustergrammer_js.txt
@@ -59,15 +59,16 @@ Clustergrammer-JS' API allows users to pass options to the front-end visualizati
 
 Clustergrammer-JSON
 ===================
-The JSON format required for Clustergrammer.js is described here:
+The visualization JSON format required for Clustergrammer.js is described here:
+
+
+Users can also generate the visualization JSON using their own scripts as long as they adhere to the above format.
 
 .. _clustergrammer_js_dev:
 
 Clustergrammer-JS Development
 =============================
-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 is built with `Webpack Module Bundler`_ from the source files in `src`_.
+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 is built with `Webpack Module Bundler`_ from the source files in the `src`_ directory.
 
 Please :ref:`contact` Nicolas Fernandez or Avi Ma'ayan with questions or use the GitHub `issues`_ feature to raise an issue.
 

diff --git a/docs/_build_html/_sources/index.txt b/docs/_build_html/_sources/index.txt
@@ -27,6 +27,7 @@ Clustergrammer was built to visualize biological data but is applicable for visu
 - `Cancer Cell Line Encyclopedia Gene Expression Data`_
 - `Zika Virus RNA-seq Data Visualization`_
 - `Single Cell RNA-seq Data Visualization`_
+- `Kinase Substrate Similarity Network`_
 - `Iris flower dataset`_
 - `MNIST Handwritten Digit Dataset`_
 
@@ -70,4 +71,5 @@ Contents:
 .. _`Zika Virus RNA-seq Data Visualization`: http://nbviewer.jupyter.org/github/maayanlab/Zika-RNAseq-Pipeline/blob/master/Zika.ipynb
 .. _`Iris flower dataset`: http://nbviewer.jupyter.org/github/MaayanLab/iris_clustergrammer_visualization/blob/master/Iris%20Dataset.ipynb
 .. _`MNIST Handwritten Digit Dataset`: https://maayanlab.github.io/MNIST_heatmaps/
-.. _`Single Cell RNA-seq Data Visualization`: http://nbviewer.jupyter.org/github/MaayanLab/single_cell_RNAseq_Visualization/blob/master/Single%20Cell%20RNAseq%20Visualization%20Example.ipynb
+.. _`Single Cell RNA-seq Data Visualization`: http://nbviewer.jupyter.org/github/MaayanLab/single_cell_RNAseq_Visualization/blob/master/Single%20Cell%20RNAseq%20Visualization%20Example.ipynb
+.. _`Kinase Substrate Similarity Network`: https://maayanlab.github.io/kinase_substrate_similarity_network/
diff --git a/docs/_build_html/app_integration.html b/docs/_build_html/app_integration.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Clustergrammer App Integrations &mdash; Clustergrammer 1.0.0 documentation</title>
+  <title>App Integration Examples &mdash; Clustergrammer 1.0.0 documentation</title>
 
 
 
@@ -92,7 +92,13 @@
 <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 current"><a class="current reference internal" href="#">Clustergrammer App Integrations</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">App Integration Examples</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="license.html">License</a></li>
 </ul>
@@ -125,7 +131,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="index.html">Docs</a> &raquo;</li>
 
-    <li>Clustergrammer App Integrations</li>
+    <li>App Integration Examples</li>
       <li class="wy-breadcrumbs-aside">
 
 
@@ -139,16 +145,25 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <div class="section" id="clustergrammer-app-integrations">
-<span id="app-integration"></span><h1>Clustergrammer App Integrations<a class="headerlink" href="#clustergrammer-app-integrations" title="Permalink to this headline">¶</a></h1>
-<p>Clustergrammer can be integrated into other web applications and is being utilized to visualize data for the following Ma&#8217;ayan lab web applications:</p>
-<ul class="simple">
-<li><a class="reference external" href="http://amp.pharm.mssm.edu/Enrichr/">Enrichr</a></li>
-<li><a class="reference external" href="http://amp.pharm.mssm.edu/gen3va/">GEN3VA</a></li>
-<li><a class="reference external" href="http://amp.pharm.mssm.edu/l1000cds2/">L1000CDS2</a></li>
-<li><a class="reference external" href="http://amp.pharm.mssm.edu/g2e/">GEO2Enrichr</a></li>
-<li><a class="reference external" href="http://amp.pharm.mssm.edu/Harmonizome/">Harmonizome</a></li>
-</ul>
+  <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 other web applications and is being utilized to visualize data for the following <a class="reference external" href="http://labs.icahn.mssm.edu/maayanlab/">Ma&#8217;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 the <a class="reference internal" href="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web App</span></a>&#8216;s API to produce dynamic heatmaps of enriched terms as columns and user lists as rows. This helps users understand the relationships between their input genes and the returned enriched terms.</p>
+</div>
+<div class="section" id="gen3va">
+<h2>GEN3VA<a class="headerlink" href="#gen3va" title="Permalink to this headline">¶</a></h2>
+<p>The gene signature analysis and visualization tool, <a class="reference external" href="http://amp.pharm.mssm.edu/gen3va/">GEN3VA</a>, uses Clustergrammer&#8217;s core libraries, <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>, to dynamcally visualize collections of gene expression signatures collected by users from <a class="reference external" href="https://www.ncbi.nlm.nih.gov/geo/">GEO</a> as interactive heatmaps. GEN3VA also uses Clustergrammer to visualize enrichment analysis results (obtained from <a class="reference external" href="http://amp.pharm.mssm.edu/Enrichr/">Enrichr</a>) and perturbations that reverse or mimic gene expression signatures (obtained from <a class="reference external" href="http://amp.pharm.mssm.edu/l1000cds2/">L1000CDS2</a>)</p>
+</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>&#8216;s API to produce interactive heatmaps of perturbagen gene signatures that mimic or reverse an input gene signature. This can be useful for users that are interested in the specific genes that are differentially regulated by the identified perturbagens.</p>
+</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 <a class="reference internal" href="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web App</span></a>&#8216;s API to generate visualize of curated biological datasets as heatmaps and adjacency matrices (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>
 </div>
 
 

diff --git a/docs/_build_html/clustergrammer_js.html b/docs/_build_html/clustergrammer_js.html
@@ -194,12 +194,12 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 </div>
 <div class="section" id="clustergrammer-json">
 <span id="id5"></span><h2>Clustergrammer-JSON<a class="headerlink" href="#clustergrammer-json" title="Permalink to this headline">¶</a></h2>
-<p>The JSON format required for Clustergrammer.js is described here:</p>
+<p>The visualization JSON format required for Clustergrammer.js is described here:</p>
+<p>Users can also generate the visualization JSON using their own scripts as long as they adhere to the above format.</p>
 </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="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>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>. Clustergrammer-JS is built with <a class="reference external" href="https://webpack.github.io/">Webpack Module Bundler</a> from the source files in the <a class="reference external" href="https://github.com/MaayanLab/clustergrammer/tree/master/src">src</a> directory.</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>
 </div>

diff --git a/docs/_build_html/genindex.html b/docs/_build_html/genindex.html
@@ -91,7 +91,7 @@
 <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="app_integration.html">Clustergrammer App Integrations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="app_integration.html">App Integration Examples</a></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="license.html">License</a></li>
 </ul>