cleaning up Getting Started

docs/_build_html/_sources/case_studies.rst.txt

@@ -1,7 +1,7 @@
 .. _case_studies:
 
-Case Studies and Examples
--------------------------
+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.
 
 Cancer Cell Line Encyclopedia Gene Expression Data

docs/_build_html/_sources/clustergrammer2.rst.txt

@@ -1,6 +1,6 @@
 .. _clustergrammer2:
 
-Clustergrammer2 Jupyter Widget
+Clustergrammer2 Widget
 ------------------------
 
 Clustergrammer2 is the new in-development WegGL Jupyter Widget. This widget can visualize much larger datasets (matrices with ~millions of matrix-cells).

docs/_build_html/_sources/getting_started.rst.txt

@@ -1,50 +1,25 @@
 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 three main 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` for more information). Clustergrammer can be used in the following ways:
 
-#. :ref:`clustergrammer_web`: `http://amp.pharm.mssm.edu/clustergrammer`_
-#. :ref:`clustergrammer_widget`
-#. :ref:`clustergrammer_js` and :ref:`clustergrammer_py` libraries
-
-This section will provide information on how to interact with the visualization and how to quickly visualize your own data using the :ref:`clustergrammer_web` and the :ref:`clustergrammer_widget`. See :ref:`case_studies` 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 :ref:`building_web_page` section.
-
-What's New
------------
-
-JupyterCon 2018
+Web application
 ===============
 
-.. raw:: html
+* :ref:`clustergrammer_web`: `http://amp.pharm.mssm.edu/clustergrammer`_
 
-         <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/82epZkmfkrE" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
-         </div>
-
-The Clustergrammer-Widget was recently presented at JupyterCon 2018.
-
-Clustergrammer2
+Jupyter Widget
 ===============
 
-.. figure:: _static/clustergrammer2_480px.gif
-  :width: 800px
-  :align: left
-  :alt: demo GIF
-  :target: https://github.com/ismms-himc/clustergrammer2-examples
-
-Clustergrammer is currently being re-built using the WebGL library `regl`_:
-
-* :ref:`clustergrammer_gl`: WebGL JavaScript Library
-* :ref:`clustergrammer2`: WebGL Jupyter Widget
+* :ref:`clustergrammer2`
+* :ref:`clustergrammer_widget`
 
-Try running the Clustergrammer2 Jupyter widget on MyBinder
+JavaScript and Python libraries
+================================
 
-|intro-notebook|
+* :ref:`clustergrammer_js` and :ref:`clustergrammer_py` libraries
 
-|ccle-notebook|
-
-and see `Clustergrammer2-Examples`_.
+This section will provide information on how to interact with the visualization and how to quickly visualize your own data using the :ref:`clustergrammer_web` and the :ref:`clustergrammer_widget`. See :ref:`case_studies` 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 :ref:`building_web_page` section.
 
 Interacting with Clustergrammer Heatmaps
 ========================================
@@ -65,12 +40,6 @@ Clustergrammer produces highly interactive visualizations that enable intuitive
 - :ref:`crop`
 - :ref:`row_search`
 
-Press play or interact with the gene-expression demo below to see some of Clustergrammer's interactive features and see :ref:`interacting_with_viz` for more information:
-
-.. raw:: html
-
-   <iframe id='iframe_preview' src="https://amp.pharm.mssm.edu/clustergrammer/demo/" frameBorder="0" style='height: 495px; width:730px; margin-bottom:15px;'></iframe>
-
 Clustergrammer also has :ref:`biology_specific_features` for working with gene-level data including:
 
 - Mouseover gene names and description look-up (using `Harmonizome`_)
@@ -117,9 +86,11 @@ Users can share their interactive visualizations using their permanent link. See
 
 .. _getting_started_widget:
 
-Clustergrammer-Widget
+Jupyter Widgets
 =====================
-`Jupyter`_ notebooks are ideal for generating reproducible workflows and analysis. They are also the best way to share Clustergrammer's interactive visualizations while providing context, analysis, and the underlying data to enable reproducibility (see :ref:`clustergrammer_widget_examples`). The :ref:`clustergrammer_widget` enables users to easily produce interactive visualizations within a Jupyter notebook that can be shared with collaborators (using `nbviewer`_). The :ref:`clustergrammer_widget` can be used to visualize a matrix of data from a matrix file or from a `Pandas`_ DataFrame (see :ref:`matrix_format_io` for more information).
+`Jupyter`_ notebooks are ideal for generating reproducible workflows and analysis. They are also the best way to share Clustergrammer's interactive visualizations while providing context, analysis, and the underlying data to enable reproducibility (see :ref:`clustergrammer_widget_examples`).
+
+:ref:`clustergrammer_widget` and :ref:`clustergrammer2` enable users to easily produce interactive visualizations within a Jupyter notebook that can be shared with collaborators (using `nbviewer`_). The :ref:`clustergrammer_widget` can be used to visualize a matrix of data from a matrix file or from a `Pandas`_ DataFrame (see :ref:`matrix_format_io` for more information).
 
 Clustergrammer has been applied to visualize and analyze a wide variety of biological and non-biological data. See the Jupyter notebook examples below and :ref:`case_studies` for more information:
 
@@ -133,39 +104,6 @@ Clustergrammer has been applied to visualize and analyze a wide variety of biolo
 - `Iris Dataset.ipynb`_
 
 
-To use the :ref:`clustergrammer_widget` users need to install: `Python`_, `Jupyter`_ notebook, the widget dependencies (see :ref:`clustergrammer_widget_dependencies`), and `ipywidgets`_ version >6.0.0 (required for saving notebook with widgets). Users can `install Anaconda`_, a Python distribution that includes the Jupyter notebook as well as other scientific computing libraries, to easily obtain the necessary dependencies (except ipywidgets version >6.0.0). Once these requirements have been met, ``clustergrammer_widget`` can then be installed (with pip) and enabled using the following commands:
-::
-
-  pip install --upgrade clustergrammer_widget
-  jupyter nbextension enable --py --sys-prefix widgetsnbextension
-  jupyter nbextension enable --py --sys-prefix clustergrammer_widget
-
-With the ``clustergrammer_widget`` installed and enabled users can visualize their data (from a file) using the following Python commands:
-::
-
-  # import clustergrammer_widgets and initialize network object
-  from clustergrammer_widget import *
-  net = Network(clustergrammer_widget)
-
-  # load matrix file and cluster using default parameters
-  net.load_file('rc_two_cats.txt')
-  net.cluster()
-
-  # make interactive widget
-  net.widget()
-
-See the screenshot below for an example widget visualization:
-
-.. figure:: _static/jupyter_widget_nbviewer.png
-  :width: 900px
-  :align: left
-  :alt: Jupyter Widget NBViewer
-  :target: http://nbviewer.jupyter.org/github/MaayanLab/clustergrammer-widget/blob/master/Running_clustergrammer_widget.ipynb
-
-  Clustergrammer can be used as an interactive widget within a Jupyter notebook and shared using nbviewer (see `Running_clustergrammer_widget.ipynb`_ example).
-
-Users can download and reproduce the example notebook, `Running_clustergrammer_widget.ipynb`_, by cloning its `GitHub repo`_. For more information about using the widget (e.g. visualizing data from a Pandas DataFrame and sharing notebooks) see :ref:`clustergrammer_widget`.
-
 
 .. _`Clustergrammer2-Examples`: https://github.com/ismms-himc/clustergrammer2-examples
 .. _`Clustergrammer2`: https://github.com/ismms-himc/clustergrammer2

docs/_build_html/_sources/index.rst.txt

@@ -97,13 +97,13 @@ Contents:
 
    getting_started
    clustergrammer_web
-   clustergrammer_widget
    clustergrammer2
    interacting_with_viz
    biology_specific_features
    case_studies
    matrix_format_io
    building_webpage
+   clustergrammer_widget
    clustergrammer_js
    clustergrammer_gl
    clustergrammer_py

docs/_build_html/case_studies.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Case Studies and Examples &mdash; Clustergrammer 1.1.0 documentation</title>
+  <title>Case Studies and Tutorials &mdash; Clustergrammer 1.1.0 documentation</title>
 
 
 
@@ -85,11 +85,12 @@
 
               <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="clustergrammer_widget.html">Clustergrammer Jupyter Widget</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 Examples</a><ul>
+<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="#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>
@@ -101,7 +102,9 @@
 </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>
 <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_gl.html">Clustergrammer-GL</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">App Integration Examples</a></li>
 <li class="toctree-l1"><a class="reference internal" href="developing_with_clustergrammer.html">Developing Clustergrammer</a></li>
@@ -151,7 +154,7 @@
 
       <li><a href="index.html">Docs</a> &raquo;</li>
 
-      <li>Case Studies and Examples</li>
+      <li>Case Studies and Tutorials</li>
 
 
       <li class="wy-breadcrumbs-aside">
@@ -170,8 +173,8 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <div class="section" id="case-studies-and-examples">
-<span id="case-studies"></span><h1>Case Studies and Examples<a class="headerlink" href="#case-studies-and-examples" title="Permalink to this headline">¶</a></h1>
+  <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="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>
@@ -214,7 +217,7 @@ <h2>Large Network: Kinase Substrate Similarity Network<a class="headerlink" href
 <h2>Machine Learning and Miscellaneous Datasets<a class="headerlink" href="#machine-learning-and-miscellaneous-datasets" title="Permalink to this headline">¶</a></h2>
 <div class="figure align-left" id="id6">
 <a class="reference external image-reference" href="http://nbviewer.jupyter.org/github/MaayanLab/MNIST_heatmaps/blob/master/notebooks/MNIST_Notebook.ipynb#Visualize-Downsampled-Version-of-MNIST"><img alt="MNIST Screenshot" src="_images/MNIST_screenshot.png" style="width: 450px;" /></a>
-<p class="caption"><span class="caption-text">Screenshot from the <a class="reference external" href="http://nbviewer.jupyter.org/github/MaayanLab/MNIST_heatmaps/blob/master/notebooks/MNIST_Notebook.ipynb">MNIST Notebook</a> that demonstrates how the <a class="reference internal" href="clustergrammer_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer Jupyter Widget</span></a> can be used to visualize the <a class="reference external" href="http://yann.lecun.com/exdb/mnist/">MNIST Data</a>. Downsampled handwritten digits (K-means downsampled from 70,0000 handwritten digits to 300 digit-clusters) are shown as columns with digit-type categories and pixels are shown as rows. For more information see the <a class="reference external" href="http://nbviewer.jupyter.org/github/MaayanLab/MNIST_heatmaps/blob/master/notebooks/MNIST_Notebook.ipynb">MNIST Notebook</a>.</span></p>
+<p class="caption"><span class="caption-text">Screenshot from the <a class="reference external" href="http://nbviewer.jupyter.org/github/MaayanLab/MNIST_heatmaps/blob/master/notebooks/MNIST_Notebook.ipynb">MNIST Notebook</a> that demonstrates how the <a class="reference internal" href="clustergrammer_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer-Widget</span></a> can be used to visualize the <a class="reference external" href="http://yann.lecun.com/exdb/mnist/">MNIST Data</a>. Downsampled handwritten digits (K-means downsampled from 70,0000 handwritten digits to 300 digit-clusters) are shown as columns with digit-type categories and pixels are shown as rows. For more information see the <a class="reference external" href="http://nbviewer.jupyter.org/github/MaayanLab/MNIST_heatmaps/blob/master/notebooks/MNIST_Notebook.ipynb">MNIST Notebook</a>.</span></p>
 </div>
 <p>Clustergrammer was used to visualize several widely used machine learning Datasets and other miscellaneous Datasets:</p>
 <ul class="simple">

docs/_build_html/clustergrammer2.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Clustergrammer2 Jupyter Widget &mdash; Clustergrammer 1.1.0 documentation</title>
+  <title>Clustergrammer2 Widget &mdash; Clustergrammer 1.1.0 documentation</title>
 
 
 
@@ -30,7 +30,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Interacting with the Visualization" href="interacting_with_viz.html" />
-    <link rel="prev" title="Clustergrammer Jupyter Widget" href="clustergrammer_widget.html" /> 
+    <link rel="prev" title="Clustergrammer Web App" href="clustergrammer_web.html" /> 
 
 
   <script src="_static/js/modernizr.min.js"></script>
@@ -86,13 +86,13 @@
               <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="clustergrammer_web.html">Clustergrammer Web App</a></li>
-<li class="toctree-l1"><a class="reference internal" href="clustergrammer_widget.html">Clustergrammer Jupyter Widget</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">Clustergrammer2 Jupyter Widget</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">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"><a class="reference internal" href="case_studies.html">Case Studies and Examples</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>
 <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_gl.html">Clustergrammer-GL</a></li>
 <li class="toctree-l1"><a class="reference internal" href="clustergrammer_py.html">Clustergrammer-PY</a></li>
@@ -144,7 +144,7 @@
 
       <li><a href="index.html">Docs</a> &raquo;</li>
 
-      <li>Clustergrammer2 Jupyter Widget</li>
+      <li>Clustergrammer2 Widget</li>
 
 
       <li class="wy-breadcrumbs-aside">
@@ -163,8 +163,8 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <div class="section" id="clustergrammer2-jupyter-widget">
-<span id="clustergrammer2"></span><h1>Clustergrammer2 Jupyter Widget<a class="headerlink" href="#clustergrammer2-jupyter-widget" title="Permalink to this headline">¶</a></h1>
+  <div class="section" id="clustergrammer2-widget">
+<span id="clustergrammer2"></span><h1>Clustergrammer2 Widget<a class="headerlink" href="#clustergrammer2-widget" title="Permalink to this headline">¶</a></h1>
 <p>Clustergrammer2 is the new in-development WegGL Jupyter Widget. This widget can visualize much larger datasets (matrices with ~millions of matrix-cells).</p>
 <p>Clustergrammer2 is being built using the WebGL library <a class="reference external" href="http://regl.party/">regl</a>, is free and open-source, and can be found on <a class="reference external" href="https://github.com/ismms-himc/clustergrammer2">GitHub</a>.</p>
 <div class="figure align-left">
@@ -188,7 +188,7 @@
         <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="clustergrammer_widget.html" class="btn btn-neutral" title="Clustergrammer Jupyter Widget" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+        <a href="clustergrammer_web.html" class="btn btn-neutral" title="Clustergrammer Web App" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
 
     </div>