rearranged names

docs/_build_html/_sources/clustergrammer_js.txt

@@ -1,4 +1,4 @@
-.. _clustergrammer_js:
+. _clustergrammer_js:
 
 Clustergrammer-JS
 -----------------
@@ -295,7 +295,7 @@ Clustergrammer-JS Development
 =============================
 The Clustergrammer-JS source code can be found in the `Clustergrammer GitHub 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 report an issue.
+Please :ref:`contact` Nicolas Fernandez and Avi Ma'ayan with questions or use the GitHub `issues`_ feature to report an issue.
 
 .. _`SVG`: https://en.wikipedia.org/wiki/Scalable_Vector_Graphics
 .. _`Clustergrammer GitHub repo`: https://github.com/MaayanLab/clustergrammer

docs/_build_html/_sources/clustergrammer_py.txt

@@ -88,7 +88,7 @@ Clustergrammer-PY Development
 =============================
 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`.
 
-Please :ref:`contact` Nicolas Fernandez or Avi Ma'ayan with questions or use the GitHub `issues`_ feature to report an issue.
+Please :ref:`contact` Nicolas Fernandez and Avi Ma'ayan with questions or use the GitHub `issues`_ feature to report an issue.
 
 .. _`GitHub repo`: http://github.com/MaayanLab/clustergrammer-py
 .. _`package index`: https://pypi.python.org/pypi?:action=display&name=clustergrammer

docs/_build_html/_sources/clustergrammer_widget.txt

@@ -140,7 +140,7 @@ Clustergrammer-Widget Development
 =================================
 Clustergrammer-Widget's source code can be found in the `clustergrammer-widget`_ GitHub repo. Clustergrammer-Widget is built using the `ipywidgets`_ framework (using the `cookie cutter`_ template).
 
-Please :ref:`contact` Nicolas Fernandez or Avi Ma'ayan with questions or use the GitHub `issues`_ feature to report an issue.
+Please :ref:`contact` Nicolas Fernandez and Avi Ma'ayan with questions or use the GitHub `issues`_ feature to report an issue.
 
 .. _`ipywidgets version 6`: https://github.com/ipython/ipywidgets/releases
 .. _`ipywidgets`: http://ipywidgets.readthedocs.io/en/latest/

docs/_build_html/_sources/index.txt

@@ -38,7 +38,7 @@ Clustergrammer was developed to visualize high-dimensional biological data (e.g.
 
 Contact
 =======
-Please contact Avi Ma'ayan (avi.maayan@mssm.edu) and Nicolas Fernandez (nicolas.fernandez@mssm.edu) for support, comments, and suggestions.
+Please contact Nicolas Fernandez (nicolas.fernandez@mssm.edu) and Avi Ma'ayan (avi.maayan@mssm.edu) for support, comments, and suggestions.
 
 Funding
 =======

docs/_build_html/_sources/license.txt

@@ -5,7 +5,7 @@ License
   :width: 350px
   :alt: Interacting with Categories
 
-Clustergrammer is being developed by the `Ma'ayan lab`_ at the `Icahn School of Medicine at Mount Sinai`_ for the `BD2K-LINCS DCIC`_ and the `KMC-IDG`_. Please contact Avi Ma'ayan (avi.maayan@mssm.edu) and Nicolas Fernandez (nicolas.fernandez@mssm.edu) with any questions about the License.
+Clustergrammer is being developed by the `Ma'ayan lab`_ at the `Icahn School of Medicine at Mount Sinai`_ for the `BD2K-LINCS DCIC`_ and the `KMC-IDG`_. Please contact Nicolas Fernandez (nicolas.fernandez@mssm.edu) and Avi Ma'ayan (avi.maayan@mssm.edu) with any questions about the License.
 
 Clustergrammer's `license`_ and third-party licenses are in the `LICENSES`_ directory.
 

docs/_build_html/clustergrammer_js.html

@@ -150,13 +150,14 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <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:</p>
+<div class="section" id="clustergrammer-js">
+<h1>Clustergrammer-JS<a class="headerlink" href="#clustergrammer-js" title="Permalink to this headline">¶</a></h1>
 <p><a class="reference external" href="https://www.npmjs.com/package/clustergrammer"><img alt="version" src="https://img.shields.io/npm/v/clustergrammer.svg" /></a>
 <a class="reference external" href="https://github.com/MaayanLab/clustergrammer/blob/master/LICENSES/LICENSE"><img alt="license" src="https://img.shields.io/npm/l/clustergrammer.svg" /></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="clustergrammer-js-dependencies">
-<span id="id2"></span><h2>Clustergrammer-JS Dependencies<a class="headerlink" href="#clustergrammer-js-dependencies" title="Permalink to this headline">¶</a></h2>
+<span id="id1"></span><h2>Clustergrammer-JS Dependencies<a class="headerlink" href="#clustergrammer-js-dependencies" title="Permalink to this headline">¶</a></h2>
 <ul class="simple">
 <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>
@@ -173,7 +174,7 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 <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 GitHub repo</a>.</p>
 </div>
 <div class="section" id="javascript-workflow-example">
-<span id="id3"></span><h2>JavaScript Workflow Example<a class="headerlink" href="#javascript-workflow-example" title="Permalink to this headline">¶</a></h2>
+<span id="id2"></span><h2>JavaScript Workflow Example<a class="headerlink" href="#javascript-workflow-example" title="Permalink to this headline">¶</a></h2>
 <p>This workflow shows how to generate a visualization using the JSON produced by Clustergrammer.py</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">//</span> <span class="n">load</span> <span class="n">visualization</span> <span class="n">JSON</span> <span class="n">to</span> <span class="n">network_data</span>
 <span class="n">var</span> <span class="n">args</span> <span class="o">=</span> <span class="p">{</span>
@@ -187,11 +188,11 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 <p>The <code class="docutils literal"><span class="pre">id</span></code> of the container where the visualization will be made is passed as <code class="docutils literal"><span class="pre">root</span></code> (this root container must be made by the user). The <a class="reference internal" href="#visualization-json"><span class="std std-ref">Visualization-JSON</span></a> contains the information necessary to generate the visualization and is passed as <code class="docutils literal"><span class="pre">network_data</span></code>. See the <a class="reference internal" href="#clustergrammer-js-api"><span class="std std-ref">Clustergrammer-JS API</span></a> for additional arguments that can be passed to Clustergrammer.js.</p>
 </div>
 <div class="section" id="example-pages">
-<span id="id4"></span><h2>Example Pages<a class="headerlink" href="#example-pages" title="Permalink to this headline">¶</a></h2>
+<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 GitHub repo</a> contains several example pages demonstrating how to build a webpage with a Clustergrammer 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. 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">
-<span id="id5"></span><h2>Clustergrammer-JS API<a class="headerlink" href="#clustergrammer-js-api" title="Permalink to this headline">¶</a></h2>
+<span id="id4"></span><h2>Clustergrammer-JS API<a class="headerlink" href="#clustergrammer-js-api" title="Permalink to this headline">¶</a></h2>
 <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>
@@ -462,7 +463,7 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 
 </div>
 <div class="section" id="visualization-json">
-<span id="id6"></span><h2>Visualization-JSON<a class="headerlink" href="#visualization-json" title="Permalink to this headline">¶</a></h2>
+<span id="id5"></span><h2>Visualization-JSON<a class="headerlink" href="#visualization-json" title="Permalink to this headline">¶</a></h2>
 <p>The visualization-JSON is calculated by <a class="reference internal" href="clustergrammer_py.html#clustergrammer-py"><span class="std std-ref">Clustergrammer-PY</span></a> and encodes everything needed for the front-end Clustergrammer-JS to produce the visualization. The visualization-JSON format is described here (see <a class="reference external" href="https://github.com/MaayanLab/clustergrammer-json/blob/master/clustergrammer_example.json">clustergrammer_example.json</a> for an example file). An overview of the format is shown below (note that the group arrays are not shown):</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="p">{</span>
   <span class="s2">&quot;row_nodes&quot;</span><span class="p">:[</span>
@@ -522,7 +523,7 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 <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>The Clustergrammer-JS source code can be found in the <a class="reference external" href="https://github.com/MaayanLab/clustergrammer">Clustergrammer GitHub repo</a>. 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">Funding and 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 report an issue.</p>
+<p>Please <a class="reference internal" href="index.html#contact"><span class="std std-ref">Contact</span></a> Nicolas Fernandez and 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 report an issue.</p>
 </div>
 </div>
 

docs/_build_html/clustergrammer_py.html

@@ -151,7 +151,7 @@
   <div class="section" id="clustergrammer-py">
 <span id="id1"></span><h1>Clustergrammer-PY<a class="headerlink" href="#clustergrammer-py" title="Permalink to this headline">¶</a></h1>
 <p><a class="reference external" href="https://pypi.python.org/pypi?:action=display&amp;name=clustergrammer"><img alt="version" src="https://img.shields.io/pypi/v/clustergrammer.svg" /></a></p>
-<p>Clustergrammer-PY is the back-end Python library that is used to hierarchically cluster the data and generate the <a class="reference internal" href="clustergrammer_js.html#visualization-json"><span class="std std-ref">Visualization-JSON</span></a> for the front end <a class="reference internal" href="clustergrammer_js.html#clustergrammer-js"><span class="std std-ref">Clustergrammer-JS</span></a> visualization library. Clustergrammer-PY is compatible with Python 2 and 3.</p>
+<p>Clustergrammer-PY is the back-end Python library that is used to hierarchically cluster the data and generate the <a class="reference internal" href="clustergrammer_js.html#visualization-json"><span class="std std-ref">Visualization-JSON</span></a> for the front end <span class="xref std std-ref">clustergrammer_js</span> visualization library. Clustergrammer-PY is compatible with Python 2 and 3.</p>
 <div class="section" id="clustergrammer-py-dependencies">
 <span id="id2"></span><h2>Clustergrammer-PY Dependencies<a class="headerlink" href="#clustergrammer-py-dependencies" title="Permalink to this headline">¶</a></h2>
 <ul class="simple">
@@ -171,7 +171,7 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 </div>
 <div class="section" id="python-workflow-examples">
 <span id="clustergrammer-py-workflow"></span><h2>Python Workflow Examples<a class="headerlink" href="#python-workflow-examples" title="Permalink to this headline">¶</a></h2>
-<p>This workflow shows how to cluster a matrix of data from a file (see <a class="reference internal" href="matrix_format_io.html#matrix-format-io"><span class="std std-ref">Matrix Formats and Input/Output</span></a>) and generate a <a class="reference internal" href="clustergrammer_js.html#visualization-json"><span class="std std-ref">Visualization-JSON</span></a> (for use by <a class="reference internal" href="clustergrammer_js.html#clustergrammer-js"><span class="std std-ref">Clustergrammer-JS</span></a>):</p>
+<p>This workflow shows how to cluster a matrix of data from a file (see <a class="reference internal" href="matrix_format_io.html#matrix-format-io"><span class="std std-ref">Matrix Formats and Input/Output</span></a>) and generate a <a class="reference internal" href="clustergrammer_js.html#visualization-json"><span class="std std-ref">Visualization-JSON</span></a> (for use by <span class="xref std std-ref">clustergrammer_js</span>):</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># make network object and load file</span>
 <span class="kn">from</span> <span class="nn">clustergrammer</span> <span class="k">import</span> <span class="n">Network</span>
 <span class="n">net</span> <span class="o">=</span> <span class="n">Network</span><span class="p">()</span>
@@ -214,7 +214,7 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 <dt id="clustergrammer_py.Network">
 <em class="property">class </em><code class="descclassname">clustergrammer_py.</code><code class="descname">Network</code><span class="sig-paren">(</span><em>widget=None</em><span class="sig-paren">)</span><a class="headerlink" href="#clustergrammer_py.Network" title="Permalink to this definition">¶</a></dt>
 <dd><p>version 1.12.4</p>
-<p>Clustergrammer.py takes a matrix as input (either from a file of a Pandas DataFrame), normalizes/filters, hierarchically clusters, and produces the <a class="reference internal" href="clustergrammer_js.html#visualization-json"><span class="std std-ref">Visualization-JSON</span></a> for <a class="reference internal" href="clustergrammer_js.html#clustergrammer-js"><span class="std std-ref">Clustergrammer-JS</span></a>.</p>
+<p>Clustergrammer.py takes a matrix as input (either from a file of a Pandas DataFrame), normalizes/filters, hierarchically clusters, and produces the <a class="reference internal" href="clustergrammer_js.html#visualization-json"><span class="std std-ref">Visualization-JSON</span></a> for <span class="xref std std-ref">clustergrammer_js</span>.</p>
 <p>Networks have two states:</p>
 <blockquote>
 <div><ol class="arabic simple">
@@ -462,7 +462,7 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 <div class="section" id="clustergrammer-py-development">
 <span id="clustergrammer-py-dev"></span><h2>Clustergrammer-PY Development<a class="headerlink" href="#clustergrammer-py-development" 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="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>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-py/issues">issues</a> feature to report an issue.</p>
+<p>Please <a class="reference internal" href="index.html#contact"><span class="std std-ref">Contact</span></a> Nicolas Fernandez and Avi Ma&#8217;ayan with questions or use the GitHub <a class="reference external" href="https://github.com/MaayanLab/clustergrammer-py/issues">issues</a> feature to report an issue.</p>
 </div>
 </div>