adding PBMC example with multiple cloud based links to re-run notebook

cornhundred · Jul 15, 2019 · 6caa88c · 6caa88c
1 parent d05e0c5
commit 6caa88c
Show file tree

Hide file tree

Showing 11 changed files with 153 additions and 33 deletions.
diff --git a/docs/_build_html/.doctrees/case_studies.doctree b/docs/_build_html/.doctrees/case_studies.doctree
diff --git a/docs/_build_html/.doctrees/environment.pickle b/docs/_build_html/.doctrees/environment.pickle
diff --git a/docs/_build_html/.doctrees/getting_started.doctree b/docs/_build_html/.doctrees/getting_started.doctree
diff --git a/docs/_build_html/_sources/case_studies.rst.txt b/docs/_build_html/_sources/case_studies.rst.txt
@@ -4,6 +4,32 @@ Case Studies and Tutorials
 --------------------------
 Clustergrammer was developed to visualize high-dimensional biological data (e.g. genome-wide expression data), but it can also generally be applied to any high-dimensional data. Below are links to several case studies and examples using Clustergrammer to explore high-dimensional data. All examples are below are publically available through GitHub.
 
+Single Cell Gene Expression 2,700 PBMC
+=======================================
+
+.. raw:: html
+
+         <div style="position: relative; padding-bottom: 10px; height: 0; overflow: hidden; max-width: 100%; height: auto;">
+
+         <iframe width="560" height="315" src="https://www.youtube.com/embed/f-snXe2Bn9Q" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
+         </div>
+
+Single cell RNA-seq (scRNA-seq) is a powerful method to interrogate gene expression across thousands of single cells. This method provides thousands of measurements (single cells) across thousands of dimensions (genes). Clustergrammer2 is used to interactively explore an example dataset of 2,700 PBMCs obtained from `10X Genomics`_. Bulk gene expression signatures of cell types obtained from `CIBERSORT`_ were used to obtain a tentative cell type for each cell. The data and code can be found on GitHub at `clustergrammer2-notebooks`_ and the notebook can be viewed and re-run on the cloud - see below.
+
+View Interactive Notebook
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+The interactive pre-run notebook can be viewed on NBVIewer.
+
+* NBViewer: `NBViewer-2700`_.
+
+Run Notebook on the Cloud
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+This notebook can be re-run and modified on the cloud using:
+
+* MyBinder: `MyBinder-2700`_
+* Kaggle: `Viz-2-700-pbmcs-with-cell-type-predictions`_, `Clustergrammer2-2-700-pbmc-notebook`_
+* Saturn Cloud: `Saturn-2700`_
+
 Cancer Cell Line Encyclopedia Gene Expression Data
 ==================================================
 
@@ -104,5 +130,12 @@ Clustergrammer was used to visualize published single-cell gene expression data:
 .. _`CCLE`: https://portals.broadinstitute.org/ccle/home
 .. _`Wang et al.`: https://f1000research.com/articles/5-1574/v1
 .. _`Olsson et al.`: http://www.nature.com/nature/journal/v537/n7622/full/nature19348.html
-
-.. _`USDA Nutrient Dataset`: http://nbviewer.jupyter.org/github/MaayanLab/USDA_Nutrients_Viz/blob/master/USDA_Nutrients.ipynb
+.. _`USDA Nutrient Dataset`: http://nbviewer.jupyter.org/github/MaayanLab/USDA_Nutrients_Viz/blob/master/USDA_Nutrients.ipynb
+.. _`10X Genomics`: https://www.10xgenomics.com/resources/datasets/
+.. _`CIBERSORT`: https://cibersort.stanford.edu/
+.. _`clustergrammer2-notebooks`: https://github.com/ismms-himc/clustergrammer2-notebooks
+.. _`Viz-2-700-pbmcs-with-cell-type-predictions`: https://www.kaggle.com/cornhundred/viz-2-700-pbmcs-with-cell-type-predictions
+.. _`Clustergrammer2-2-700-pbmc-notebook`: https://www.kaggle.com/cornhundred/clustergrammer2-2-700-pbmc-notebook
+.. _`MyBinder-2700`: https://mybinder.org/v2/gh/ismms-himc/clustergrammer2_examples/master?filepath=notebooks%2F3.0_10X_Genomics_2700_Dataset.ipynb
+.. _`NBViewer-2700`: https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/3.0_10X_Genomics_2700_Dataset_NBViewer.ipynb
+.. _`Saturn-2700`: https://www.saturncloud.io/published/cornhundred/clustergrammer2-notebooks/notebooks/pbmc_2700_scRNA-seq/1.0_PBMC_2700_scRNA-seq.ipynb
diff --git a/docs/_build_html/_sources/getting_started.rst.txt b/docs/_build_html/_sources/getting_started.rst.txt
@@ -1,21 +1,29 @@
 Getting Started
 ---------------
 
-Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps (see :ref:`intro_heatmap_clustergram` for more information). Clustergrammer can be used in the following ways:
+Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps (see :ref:`intro_heatmap_clustergram`).
+
+Using Clustergrammer
+====================
 
 Web application
-===============
+~~~~~~~~~~~~~~~
 
 * :ref:`clustergrammer_web`: `http://amp.pharm.mssm.edu/clustergrammer`_
 
+
 Jupyter Widget
-===============
+~~~~~~~~~~~~~~~
 
 * :ref:`clustergrammer2`
+
+  * WebGL for larger datasets (e.g. scRNA-seq)
 * :ref:`clustergrammer_widget`
 
+  * SVG for smaller datasets (e.g. bulk RNA-seq)
+
 JavaScript and Python libraries
-================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 * :ref:`clustergrammer_js` and :ref:`clustergrammer_py` libraries
 

diff --git a/docs/_build_html/case_studies.html b/docs/_build_html/case_studies.html
@@ -29,8 +29,8 @@
   <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="Matrix Formats and Input/Output" href="matrix_format_io.html" />
-    <link rel="prev" title="Biology-Specific Features" href="biology_specific_features.html" /> 
+    <link rel="next" title="Interacting with the Visualization" href="interacting_with_viz.html" />
+    <link rel="prev" title="Clustergrammer2 Widget" href="clustergrammer2.html" /> 
 
 
   <script src="_static/js/modernizr.min.js"></script>
@@ -85,12 +85,14 @@
 
               <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="getting_started.html#what-s-new">What’s New</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="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 current"><a class="current reference internal" href="#">Case Studies and Tutorials</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#single-cell-gene-expression-2-700-pbmc">Single Cell Gene Expression 2,700 PBMC</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#view-interactive-notebook">View Interactive Notebook</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#run-notebook-on-the-cloud">Run Notebook on the Cloud</a></li>
+</ul>
+</li>
 <li class="toctree-l2"><a class="reference internal" href="#cancer-cell-line-encyclopedia-gene-expression-data">Cancer Cell Line Encyclopedia Gene Expression Data</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#lung-cancer-post-translational-modification-and-gene-expression-regulation">Lung Cancer Post-Translational Modification and Gene Expression Regulation</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#cytof-data-single-cell-immune-response-to-pma-treatment">CyTOF Data: Single Cell Immune Response to PMA Treatment</a></li>
@@ -100,6 +102,8 @@
 <li class="toctree-l2"><a class="reference internal" href="#single-cell-rna-seq-data-visualization">Single-Cell RNA-seq Data Visualization</a></li>
 </ul>
 </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="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="clustergrammer_widget.html">Clustergrammer-Widget</a></li>
@@ -176,6 +180,29 @@
   <div class="section" id="case-studies-and-tutorials">
 <span id="case-studies"></span><h1>Case Studies and Tutorials<a class="headerlink" href="#case-studies-and-tutorials" title="Permalink to this headline">¶</a></h1>
 <p>Clustergrammer was developed to visualize high-dimensional biological data (e.g. genome-wide expression data), but it can also generally be applied to any high-dimensional data. Below are links to several case studies and examples using Clustergrammer to explore high-dimensional data. All examples are below are publically available through GitHub.</p>
+<div class="section" id="single-cell-gene-expression-2-700-pbmc">
+<h2>Single Cell Gene Expression 2,700 PBMC<a class="headerlink" href="#single-cell-gene-expression-2-700-pbmc" title="Permalink to this headline">¶</a></h2>
+<div style="position: relative; padding-bottom: 10px; height: 0; overflow: hidden; max-width: 100%; height: auto;">
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/f-snXe2Bn9Q" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
+</div><p>Single cell RNA-seq (scRNA-seq) is a powerful method to interrogate gene expression across thousands of single cells. This method provides thousands of measurements (single cells) across thousands of dimensions (genes). Clustergrammer2 is used to interactively explore an example dataset of 2,700 PBMCs obtained from <a class="reference external" href="https://www.10xgenomics.com/resources/datasets/">10X Genomics</a>. Bulk gene expression signatures of cell types obtained from <a class="reference external" href="https://cibersort.stanford.edu/">CIBERSORT</a> were used to obtain a tentative cell type for each cell. The data and code can be found on GitHub at <a class="reference external" href="https://github.com/ismms-himc/clustergrammer2-notebooks">clustergrammer2-notebooks</a> and the notebook can be viewed and re-run on the cloud - see below.</p>
+<div class="section" id="view-interactive-notebook">
+<h3>View Interactive Notebook<a class="headerlink" href="#view-interactive-notebook" title="Permalink to this headline">¶</a></h3>
+<p>The interactive pre-run notebook can be viewed on NBVIewer.</p>
+<ul class="simple">
+<li>NBViewer: <a class="reference external" href="https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/3.0_10X_Genomics_2700_Dataset_NBViewer.ipynb">NBViewer-2700</a>.</li>
+</ul>
+</div>
+<div class="section" id="run-notebook-on-the-cloud">
+<h3>Run Notebook on the Cloud<a class="headerlink" href="#run-notebook-on-the-cloud" title="Permalink to this headline">¶</a></h3>
+<p>This notebook can be re-run and modified on the cloud using:</p>
+<ul class="simple">
+<li>MyBinder: <a class="reference external" href="https://mybinder.org/v2/gh/ismms-himc/clustergrammer2_examples/master?filepath=notebooks%2F3.0_10X_Genomics_2700_Dataset.ipynb">MyBinder-2700</a></li>
+<li>Kaggle: <a class="reference external" href="https://www.kaggle.com/cornhundred/viz-2-700-pbmcs-with-cell-type-predictions">Viz-2-700-pbmcs-with-cell-type-predictions</a>, <a class="reference external" href="https://www.kaggle.com/cornhundred/clustergrammer2-2-700-pbmc-notebook">Clustergrammer2-2-700-pbmc-notebook</a></li>
+<li>Saturn Cloud: <a class="reference external" href="https://www.saturncloud.io/published/cornhundred/clustergrammer2-notebooks/notebooks/pbmc_2700_scRNA-seq/1.0_PBMC_2700_scRNA-seq.ipynb">Saturn-2700</a></li>
+</ul>
+</div>
+</div>
 <div class="section" id="cancer-cell-line-encyclopedia-gene-expression-data">
 <h2>Cancer Cell Line Encyclopedia Gene Expression Data<a class="headerlink" href="#cancer-cell-line-encyclopedia-gene-expression-data" title="Permalink to this headline">¶</a></h2>
 <div class="figure align-left" id="id2">
@@ -245,10 +272,10 @@ <h2>Single-Cell RNA-seq Data Visualization<a class="headerlink" href="#single-ce
 
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
-        <a href="matrix_format_io.html" class="btn btn-neutral float-right" title="Matrix Formats and Input/Output" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+        <a href="interacting_with_viz.html" class="btn btn-neutral float-right" title="Interacting with the Visualization" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
-        <a href="biology_specific_features.html" class="btn btn-neutral" title="Biology-Specific Features" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+        <a href="clustergrammer2.html" class="btn btn-neutral" title="Clustergrammer2 Widget" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
 
     </div>
 

diff --git a/docs/_build_html/getting_started.html b/docs/_build_html/getting_started.html
@@ -85,19 +85,22 @@
 
               <ul class="current">
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Getting Started</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#web-application">Web application</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#jupyter-widget">Jupyter Widget</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#javascript-and-python-libraries">JavaScript and Python libraries</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#using-clustergrammer">Using Clustergrammer</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#web-application">Web application</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#jupyter-widget">Jupyter Widget</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#javascript-and-python-libraries">JavaScript and Python libraries</a></li>
+</ul>
+</li>
 <li class="toctree-l2"><a class="reference internal" href="#interacting-with-clustergrammer-heatmaps">Interacting with Clustergrammer Heatmaps</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#clustergrammer-web-app">Clustergrammer Web-App</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#jupyter-widgets">Jupyter Widgets</a></li>
 </ul>
 </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="clustergrammer2.html">Clustergrammer2 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="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 Tutorials</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="clustergrammer_widget.html">Clustergrammer-Widget</a></li>
@@ -173,27 +176,36 @@
 
   <div class="section" id="getting-started">
 <h1>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
-<p>Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps (see <a class="reference internal" href="interacting_with_viz.html#intro-heatmap-clustergram"><span class="std std-ref">Introduction to Clustergrams</span></a> for more information). Clustergrammer can be used in the following ways:</p>
+<p>Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps (see <a class="reference internal" href="interacting_with_viz.html#intro-heatmap-clustergram"><span class="std std-ref">Introduction to Clustergrams</span></a>).</p>
+<div class="section" id="using-clustergrammer">
+<h2>Using Clustergrammer<a class="headerlink" href="#using-clustergrammer" title="Permalink to this headline">¶</a></h2>
 <div class="section" id="web-application">
-<h2>Web application<a class="headerlink" href="#web-application" title="Permalink to this headline">¶</a></h2>
+<h3>Web application<a class="headerlink" href="#web-application" title="Permalink to this headline">¶</a></h3>
 <ul class="simple">
 <li><a class="reference internal" href="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web App</span></a>: <a class="reference external" href="http://amp.pharm.mssm.edu/clustergrammer/">http://amp.pharm.mssm.edu/clustergrammer</a></li>
 </ul>
 </div>
 <div class="section" id="jupyter-widget">
-<h2>Jupyter Widget<a class="headerlink" href="#jupyter-widget" title="Permalink to this headline">¶</a></h2>
+<h3>Jupyter Widget<a class="headerlink" href="#jupyter-widget" title="Permalink to this headline">¶</a></h3>
 <ul class="simple">
-<li><a class="reference internal" href="clustergrammer2.html#clustergrammer2"><span class="std std-ref">Clustergrammer2 Widget</span></a></li>
-<li><a class="reference internal" href="clustergrammer_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer-Widget</span></a></li>
+<li><a class="reference internal" href="clustergrammer2.html#clustergrammer2"><span class="std std-ref">Clustergrammer2 Widget</span></a><ul>
+<li>WebGL for larger datasets (e.g. scRNA-seq)</li>
+</ul>
+</li>
+<li><a class="reference internal" href="clustergrammer_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer-Widget</span></a><ul>
+<li>SVG for smaller datasets (e.g. bulk RNA-seq)</li>
+</ul>
+</li>
 </ul>
 </div>
 <div class="section" id="javascript-and-python-libraries">
-<h2>JavaScript and Python libraries<a class="headerlink" href="#javascript-and-python-libraries" title="Permalink to this headline">¶</a></h2>
+<h3>JavaScript and Python libraries<a class="headerlink" href="#javascript-and-python-libraries" title="Permalink to this headline">¶</a></h3>
 <ul class="simple">
 <li><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</li>
 </ul>
 <p>This section will provide information on how to interact with the visualization and how to quickly visualize your own data using 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-Widget</span></a>. See <a class="reference internal" href="case_studies.html#case-studies"><span class="std std-ref">Case Studies and Tutorials</span></a> for examples of how Clustergrammer can be used to explore and analyze real world data. For developers interested in building their own web page using Clustergrammer, please refer to the <a class="reference internal" href="building_webpage.html#building-web-page"><span class="std std-ref">Web-Development with Clustergrammer</span></a> section.</p>
 </div>
+</div>
 <div class="section" id="interacting-with-clustergrammer-heatmaps">
 <h2>Interacting with Clustergrammer Heatmaps<a class="headerlink" href="#interacting-with-clustergrammer-heatmaps" title="Permalink to this headline">¶</a></h2>
 <div class="figure align-left">