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| <!DOCTYPE html> | ||
| <!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> | ||
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| <meta name="viewport" content="width=device-width, initial-scale=1.0"> | ||
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| <title>Clustergrammer Web App — Clustergrammer 1.0.0 documentation</title> | ||
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| <link rel="top" title="Clustergrammer 1.0.0 documentation" href="index.html"/> | ||
| <link rel="next" title="Clustergrammer Jupyter Widget" href="jupyter_widget.html"/> | ||
| <link rel="prev" title="Getting Started" href="getting_started.html"/> | ||
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| <a href="index.html" class="icon icon-home"> Clustergrammer | ||
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| </a> | ||
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| <div class="version"> | ||
| 1.0.0 | ||
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| <li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting Started</a></li> | ||
| <li class="toctree-l1 current"><a class="current reference internal" href="#">Clustergrammer Web App</a><ul> | ||
| <li class="toctree-l2"><a class="reference internal" href="#uploading-data-through-the-homepage">Uploading Data through the Homepage</a></li> | ||
| <li class="toctree-l2"><a class="reference internal" href="#clustergrammer-web-visualization">Clustergrammer-Web Visualization</a></li> | ||
| <li class="toctree-l2"><a class="reference internal" href="#clustergrammer-web-api">Clustergrammer-Web API</a></li> | ||
| <li class="toctree-l2"><a class="reference internal" href="#clustergrammer-web-development">Clustergrammer-Web Development</a></li> | ||
| </ul> | ||
| </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> | ||
| <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="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> | ||
| <li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li> | ||
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| <div class="section" id="clustergrammer-web-app"> | ||
| <span id="clustergrammer-web"></span><h1>Clustergrammer Web App<a class="headerlink" href="#clustergrammer-web-app" title="Permalink to this headline">¶</a></h1> | ||
| <p><a class="reference external" href="https://github.com/MaayanLab/clustergrammer-web"><img alt="version" src="https://img.shields.io/github/release/MaayanLab/clustergrammer-web.svg" /></a></p> | ||
| <p>The Clustergrammer web application (referred to as Clustergrammer-Web) enables users to easily generate interactive and shareable heatmap visualizations.</p> | ||
| <div class="section" id="uploading-data-through-the-homepage"> | ||
| <span id="clustergrammer-web-upload"></span><h2>Uploading Data through the Homepage<a class="headerlink" href="#uploading-data-through-the-homepage" title="Permalink to this headline">¶</a></h2> | ||
| <p><strong>add upload screenshots</strong></p> | ||
| </div> | ||
| <div class="section" id="clustergrammer-web-visualization"> | ||
| <span id="clustergrammer-web-viz"></span><h2>Clustergrammer-Web Visualization<a class="headerlink" href="#clustergrammer-web-visualization" title="Permalink to this headline">¶</a></h2> | ||
| <p>Uploading a matrix to Clustergrammer-Web will redirect the user to a new permanent and shareable page with three views of their data:</p> | ||
| <ol class="arabic simple"> | ||
| <li>clustered heatmap view of their matrix</li> | ||
| <li>clustered similarity matrix of the columns in their original matrix</li> | ||
| <li>clustered similarity matrix of the rows in their original matrix</li> | ||
| </ol> | ||
| </div> | ||
| <div class="section" id="clustergrammer-web-api"> | ||
| <span id="id1"></span><h2>Clustergrammer-Web API<a class="headerlink" href="#clustergrammer-web-api" title="Permalink to this headline">¶</a></h2> | ||
| <p>Clustergrammer-Web’s RESful API enables users to programatically generate visualizations. The API can be useful for users that need to generate many clustergrams or developers that need to automatically generate visualizations for their own web application.</p> | ||
| <p><em>Matrix Upload</em></p> | ||
| <p>Users can post a matrix file to Clustergrammer-Web using the endpoint</p> | ||
| <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">amp</span><span class="o">.</span><span class="n">pharm</span><span class="o">.</span><span class="n">mssm</span><span class="o">.</span><span class="n">edu</span><span class="o">/</span><span class="n">clustergrammer</span><span class="o">/</span><span class="n">matrix_upload</span><span class="o">/</span> | ||
| </pre></div> | ||
| </div> | ||
| <p>and receive a permanent link to their visualization. Below is an example in Python 2.7 showing the post request and how to obtain the link from the response object:</p> | ||
| <div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">requests</span> | ||
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| <span class="n">filename</span> <span class="o">=</span> <span class="s1">'example_matrix.txt'</span> | ||
| <span class="n">upload_url</span> <span class="o">=</span> <span class="s1">'http://amp.pharm.mssm.edu/clustergrammer/matrix_upload/'</span> | ||
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| <span class="n">r</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">post</span><span class="p">(</span><span class="n">upload_url</span><span class="p">,</span> <span class="n">files</span><span class="o">=</span><span class="p">{</span><span class="s1">'file'</span><span class="p">:</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">'rb'</span><span class="p">)})</span> | ||
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| <span class="n">link</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">text</span> | ||
| </pre></div> | ||
| </div> | ||
| </div> | ||
| <div class="section" id="clustergrammer-web-development"> | ||
| <span id="clustergrammer-web-dev"></span><h2>Clustergrammer-Web Development<a class="headerlink" href="#clustergrammer-web-development" title="Permalink to this headline">¶</a></h2> | ||
| <p>Clustergrammer-Web is a <a class="reference external" href="https://docs.docker.com/">dockerized</a> web application built using the Python library <a class="reference external" href="http://flask.pocoo.org/">Flask</a>. Clustergrammer-Web uses the <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 and the source code can be found in the <a class="reference external" href="https://github.com/MaayanLab/clustergrammer-web/">clustergrammer-web</a> GitHub repo.</p> | ||
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| © Copyright 2017, Nicolas F. Fernandez. | ||
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