improving clustergrammer_web section

docs/_build_html/_sources/clustergrammer_web.txt

@@ -4,20 +4,23 @@ Clustergrammer Web App
 ----------------------
 |github-version|
 
-The `Web App`_ (`http://amp.pharm.mssm.edu/clustergrammer/`_) enables users to easily generate interactive and shareable heatmap visualizations by uploading their data as a tab-separated file.
+The `Web App`_ (`http://amp.pharm.mssm.edu/clustergrammer`_) enables users to easily generate interactive and shareable heatmap visualizations by uploading their data as a tab-separated file.
 
 .. _clustergrammer_web_upload:
 
 Uploading Data using the Web App Homepage
 =========================================
 
+Users can easily generate an interactive and shareable heatmap visualization using the :ref:`clustergrammer_web` (see upload section screenshot below). Simply upload a tab-separated matrix file (see :ref:`matrix_format_io` for more information) at the `homepage`_ to be redirected to a permanent and shareable visualization of your data.
+
+
 .. figure:: _static/clustergrammer_web_upload.png
   :width: 900px
   :align: left
   :alt: Clustergrammer Web
   :target: http://amp.pharm.mssm.edu/clustergrammer/
 
-  Users can easily generate an interactive and shareable heatmap visualization using the `Web App`_. Simply upload a tab-separated matrix file in the homepage to be redirected to a permanent and shareable visualization of your data.
+  Users can upload their data using the web app `homepage`_. Simply choose your file and upload to be redirected to your permanent and shareable visualization.
 
 
 .. _clustergrammer_web_viz:
@@ -26,9 +29,9 @@ Clustergrammer-Web Visualization
 ================================
 Uploading a matrix to the `Web App`_ will redirect the user to a new permanent and shareable page with three views of their data:
 
-#. clustered heatmap view of their matrix
-#. clustered similarity matrix of the columns in their original matrix
-#. clustered similarity matrix of the rows in their original matrix
+- Heatmap view of their matrix
+- Similarity matrix of the columns in their original matrix
+- Similarity matrix of the rows in their original matrix
 
 See the screenshots below and the `example visualization`_ for an example `Web App`_ visualization page.
 
@@ -92,7 +95,8 @@ Clustergrammer-Web is a `dockerized`_ Web application built using the Python lib
 .. _`clustergrammer-web`: https://github.com/MaayanLab/clustergrammer-web/
 .. _`MongoDB`: https://www.mongodb.com/
 .. _`example visualization`: http://amp.pharm.mssm.edu/clustergrammer/viz_sim_mats/58a492b4a63cb826f0be6476/rc_two_cats.txt
-.. _`http://amp.pharm.mssm.edu/clustergrammer/`: http://amp.pharm.mssm.edu/clustergrammer/
+.. _`http://amp.pharm.mssm.edu/clustergrammer`: http://amp.pharm.mssm.edu/clustergrammer/
+.. _`homepage`: http://amp.pharm.mssm.edu/clustergrammer/
 
 .. |github-version| image:: https://img.shields.io/github/release/MaayanLab/clustergrammer-web.svg
     :alt: version

docs/_build_html/_sources/getting_started.txt

@@ -114,8 +114,8 @@ Press play or interact with the gene-expression demo below to see some of Cluste
 
 Clustergrammer also has :ref:`biology_specific_features` for working with gene-level data including:
 
-- mouseover gene names and description look-up (using `Harmonizome`_)
-- enrichment analysis to find biological information (e.g. up-stream transcription factors) specific to your set of genes (using `Enrichr`_)
+- Mouseover gene names and description look-up (using `Harmonizome`_)
+- Enrichment analysis to find biological information (e.g. up-stream transcription factors) specific to your set of genes (using `Enrichr`_)
 
 
 .. _`example visualization`: http://amp.pharm.mssm.edu/clustergrammer/viz_sim_mats/58a492b4a63cb826f0be6476/rc_two_cats.txt

docs/_build_html/clustergrammer_web.html

@@ -150,22 +150,23 @@
   <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 <a class="reference external" href="http://amp.pharm.mssm.edu/clustergrammer/">Web App</a> (<a class="reference external" href="http://amp.pharm.mssm.edu/clustergrammer/">http://amp.pharm.mssm.edu/clustergrammer/</a>) enables users to easily generate interactive and shareable heatmap visualizations by uploading their data as a tab-separated file.</p>
+<p>The <a class="reference external" href="http://amp.pharm.mssm.edu/clustergrammer/">Web App</a> (<a class="reference external" href="http://amp.pharm.mssm.edu/clustergrammer/">http://amp.pharm.mssm.edu/clustergrammer</a>) enables users to easily generate interactive and shareable heatmap visualizations by uploading their data as a tab-separated file.</p>
 <div class="section" id="uploading-data-using-the-web-app-homepage">
 <span id="clustergrammer-web-upload"></span><h2>Uploading Data using the Web App Homepage<a class="headerlink" href="#uploading-data-using-the-web-app-homepage" title="Permalink to this headline">¶</a></h2>
+<p>Users can easily generate an interactive and shareable heatmap visualization using the <a class="reference internal" href="#clustergrammer-web"><span class="std std-ref">Clustergrammer Web App</span></a> (see upload section screenshot below). Simply upload a tab-separated matrix 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> for more information) at the <a class="reference external" href="http://amp.pharm.mssm.edu/clustergrammer/">homepage</a> to be redirected to a permanent and shareable visualization of your data.</p>
 <div class="figure align-left" id="id3">
 <a class="reference external image-reference" href="http://amp.pharm.mssm.edu/clustergrammer/"><img alt="Clustergrammer Web" src="_images/clustergrammer_web_upload.png" style="width: 900px;" /></a>
-<p class="caption"><span class="caption-text">Users can easily generate an interactive and shareable heatmap visualization using the <a class="reference external" href="http://amp.pharm.mssm.edu/clustergrammer/">Web App</a>. Simply upload a tab-separated matrix file in the homepage to be redirected to a permanent and shareable visualization of your data.</span></p>
+<p class="caption"><span class="caption-text">Users can upload their data using the web app <a class="reference external" href="http://amp.pharm.mssm.edu/clustergrammer/">homepage</a>. Simply choose your file and upload to be redirected to your permanent and shareable visualization.</span></p>
 </div>
 </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 the <a class="reference external" href="http://amp.pharm.mssm.edu/clustergrammer/">Web App</a> 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>
+<ul class="simple">
+<li>Heatmap view of their matrix</li>
+<li>Similarity matrix of the columns in their original matrix</li>
+<li>Similarity matrix of the rows in their original matrix</li>
+</ul>
 <p>See the screenshots below and the <a class="reference external" href="http://amp.pharm.mssm.edu/clustergrammer/viz_sim_mats/58a492b4a63cb826f0be6476/rc_two_cats.txt">example visualization</a> for an example <a class="reference external" href="http://amp.pharm.mssm.edu/clustergrammer/">Web App</a> visualization page.</p>
 <p><strong>Heatmap View</strong></p>
 <div class="figure align-left" id="id4">

docs/_build_html/getting_started.html

@@ -226,8 +226,8 @@ <h2>Interacting with Clustergrammer<a class="headerlink" href="#interacting-with
 <p>Press play or interact with the gene-expression demo below to see some of Clustergrammer&#8217;s interactive features and see <a class="reference internal" href="interacting_with_viz.html#interacting-with-viz"><span class="std std-ref">Interacting with the Visualization</span></a> for more information:</p>
 <iframe id='iframe_preview' src="https://amp.pharm.mssm.edu/clustergrammer/demo/" frameBorder="0" style='height: 495px; width:730px; margin-bottom:15px;'></iframe><p>Clustergrammer also has <a class="reference internal" href="biology_specific_features.html#biology-specific-features"><span class="std std-ref">Biology-Specific Features</span></a> for working with gene-level data including:</p>
 <ul class="simple">
-<li>mouseover gene names and description look-up (using <a class="reference external" href="http://amp.pharm.mssm.edu/Harmonizome/">Harmonizome</a>)</li>
-<li>enrichment analysis to find biological information (e.g. up-stream transcription factors) specific to your set of genes (using <a class="reference external" href="http://amp.pharm.mssm.edu/Enrichr/">Enrichr</a>)</li>
+<li>Mouseover gene names and description look-up (using <a class="reference external" href="http://amp.pharm.mssm.edu/Harmonizome/">Harmonizome</a>)</li>
+<li>Enrichment analysis to find biological information (e.g. up-stream transcription factors) specific to your set of genes (using <a class="reference external" href="http://amp.pharm.mssm.edu/Enrichr/">Enrichr</a>)</li>
 </ul>
 </div>
 </div>

docs/clustergrammer_web.rst

@@ -4,20 +4,23 @@ Clustergrammer Web App
 ----------------------
 |github-version|
 
-The `Web App`_ (`http://amp.pharm.mssm.edu/clustergrammer/`_) enables users to easily generate interactive and shareable heatmap visualizations by uploading their data as a tab-separated file.
+The `Web App`_ (`http://amp.pharm.mssm.edu/clustergrammer`_) enables users to easily generate interactive and shareable heatmap visualizations by uploading their data as a tab-separated file.
 
 .. _clustergrammer_web_upload:
 
 Uploading Data using the Web App Homepage
 =========================================
 
+Users can easily generate an interactive and shareable heatmap visualization using the :ref:`clustergrammer_web` (see upload section screenshot below). Simply upload a tab-separated matrix file (see :ref:`matrix_format_io` for more information) at the `homepage`_ to be redirected to a permanent and shareable visualization of your data.
+
+
 .. figure:: _static/clustergrammer_web_upload.png
   :width: 900px
   :align: left
   :alt: Clustergrammer Web
   :target: http://amp.pharm.mssm.edu/clustergrammer/
 
-  Users can easily generate an interactive and shareable heatmap visualization using the `Web App`_. Simply upload a tab-separated matrix file in the homepage to be redirected to a permanent and shareable visualization of your data.
+  Users can upload their data using the web app `homepage`_. Simply choose your file and upload to be redirected to your permanent and shareable visualization.
 
 
 .. _clustergrammer_web_viz:
@@ -26,9 +29,9 @@ Clustergrammer-Web Visualization
 ================================
 Uploading a matrix to the `Web App`_ will redirect the user to a new permanent and shareable page with three views of their data:
 
-#. clustered heatmap view of their matrix
-#. clustered similarity matrix of the columns in their original matrix
-#. clustered similarity matrix of the rows in their original matrix
+- Heatmap view of their matrix
+- Similarity matrix of the columns in their original matrix
+- Similarity matrix of the rows in their original matrix
 
 See the screenshots below and the `example visualization`_ for an example `Web App`_ visualization page.
 
@@ -92,7 +95,8 @@ Clustergrammer-Web is a `dockerized`_ Web application built using the Python lib
 .. _`clustergrammer-web`: https://github.com/MaayanLab/clustergrammer-web/
 .. _`MongoDB`: https://www.mongodb.com/
 .. _`example visualization`: http://amp.pharm.mssm.edu/clustergrammer/viz_sim_mats/58a492b4a63cb826f0be6476/rc_two_cats.txt
-.. _`http://amp.pharm.mssm.edu/clustergrammer/`: http://amp.pharm.mssm.edu/clustergrammer/
+.. _`http://amp.pharm.mssm.edu/clustergrammer`: http://amp.pharm.mssm.edu/clustergrammer/
+.. _`homepage`: http://amp.pharm.mssm.edu/clustergrammer/
 
 .. |github-version| image:: https://img.shields.io/github/release/MaayanLab/clustergrammer-web.svg
     :alt: version

docs/getting_started.rst

@@ -114,8 +114,8 @@ Press play or interact with the gene-expression demo below to see some of Cluste
 
 Clustergrammer also has :ref:`biology_specific_features` for working with gene-level data including:
 
-- mouseover gene names and description look-up (using `Harmonizome`_)
-- enrichment analysis to find biological information (e.g. up-stream transcription factors) specific to your set of genes (using `Enrichr`_)
+- Mouseover gene names and description look-up (using `Harmonizome`_)
+- Enrichment analysis to find biological information (e.g. up-stream transcription factors) specific to your set of genes (using `Enrichr`_)
 
 
 .. _`example visualization`: http://amp.pharm.mssm.edu/clustergrammer/viz_sim_mats/58a492b4a63cb826f0be6476/rc_two_cats.txt