spelling changes and small updates

cornhundred · Nov 18, 2018 · c4cac01 · c4cac01
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diff --git a/clustergrammer_py/__init__.py b/clustergrammer_py/__init__.py
@@ -204,7 +204,7 @@ def widget_df(self):
     '''
     Export a DataFrame from the front-end visualization. For instance, a user
     can filter to show only a single cluster using the dendrogram and then
-    get a dataframe of this cluster using the widget_df method.
+    get a DataFrame of this cluster using the widget_df method.
     '''
 
     if hasattr(self, 'widget_instance') == True:
@@ -379,7 +379,7 @@ def Iframe_web_app(self, filename=None, width=1000, height=800):
   def enrichrgram(self, lib, axis='row'):
     '''
     Add Enrichr gene enrichment results to your visualization (where your rows
-    are genes). Run enrichrgram before clustering to incldue enrichment results
+    are genes). Run enrichrgram before clustering to include enrichment results
     as row categories. Enrichrgram can also be run on the front-end using the
     Enrichr logo at the top left.
 

diff --git a/clustergrammer_py/__pycache__/__init__.cpython-36.pyc b/clustergrammer_py/__pycache__/__init__.cpython-36.pyc
diff --git a/docs/_build_html/.buildinfo b/docs/_build_html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 81c9b51177b5303ea79ecb53e3f513f7
+config: d1071f1a259f089e911f08368077683e
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build_html/.doctrees/biology_specific_features.doctree b/docs/_build_html/.doctrees/biology_specific_features.doctree
diff --git a/docs/_build_html/.doctrees/building_webpage.doctree b/docs/_build_html/.doctrees/building_webpage.doctree
diff --git a/docs/_build_html/.doctrees/clustergrammer_js.doctree b/docs/_build_html/.doctrees/clustergrammer_js.doctree
diff --git a/docs/_build_html/.doctrees/clustergrammer_py.doctree b/docs/_build_html/.doctrees/clustergrammer_py.doctree
diff --git a/docs/_build_html/.doctrees/clustergrammer_widget.doctree b/docs/_build_html/.doctrees/clustergrammer_widget.doctree
diff --git a/docs/_build_html/.doctrees/environment.pickle b/docs/_build_html/.doctrees/environment.pickle
diff --git a/docs/_build_html/.doctrees/index.doctree b/docs/_build_html/.doctrees/index.doctree
diff --git a/docs/_build_html/_sources/biology_specific_features.rst.txt b/docs/_build_html/_sources/biology_specific_features.rst.txt
@@ -43,7 +43,7 @@ Enrichrgram enables users to find biological information specific to their genes
 
 **Enrichrgram Front End**
 
-Enrichrgram on the front end is available to anyone viewing the visualization and can be used by simply clicking the red DNA-like Enrichr logo on the top left of the heatmap, which brings up a list of Enrichr libraries to choose from. To perform enrichment analysis, choose a library and Enrichrgram will return enriched terms from this library that are specifically associated with your list of genes (P-value bars indicate the degree of specificity). For instance, clicking on *ChEA 2016* will calculate enrichment for up-stream transcription factors. The enriched terms are shown as row categoris, which enables users to see which genes are associated with each term. Row-category titles show the enriched term and the red-bars represent the significance of the enrichment (see `Enrichr combined score`_). Users can run enrichment analysis on a specific cluster of genes by filtering the matrix to only show only their genes of interest. This filtering can be done using the Dendrogram Crop buttons (see :ref:`interactive_dendrogram`) or Brush-Crop button (see :ref:`crop`) to select a subset of genes for analysis.
+Enrichrgram on the front end is available to anyone viewing the visualization and can be used by simply clicking the red DNA-like Enrichr logo on the top left of the heatmap, which brings up a list of Enrichr libraries to choose from. To perform enrichment analysis, choose a library and Enrichrgram will return enriched terms from this library that are specifically associated with your list of genes (P-value bars indicate the degree of specificity). For instance, clicking on *ChEA 2016* will calculate enrichment for up-stream transcription factors. The enriched terms are shown as row categories, which enables users to see which genes are associated with each term. Row-category titles show the enriched term and the red-bars represent the significance of the enrichment (see `Enrichr combined score`_). Users can run enrichment analysis on a specific cluster of genes by filtering the matrix to only show only their genes of interest. This filtering can be done using the Dendrogram Crop buttons (see :ref:`interactive_dendrogram`) or Brush-Crop button (see :ref:`crop`) to select a subset of genes for analysis.
 
 .. figure:: _static/enrichrgram_results.png
   :width: 900px

diff --git a/docs/_build_html/_sources/building_webpage.rst.txt b/docs/_build_html/_sources/building_webpage.rst.txt
@@ -31,7 +31,7 @@ To make a page, simply include the :ref:`clustergrammer_js` script in your page
 Jupyter Notebook Webpages
 =========================
 
-The :ref:`clustergrammer_widget` can also be used in combination with `nbviewer`_ to share static Jupyter notebook webpages with embedded interactive Clustergrammer visualizations. This is one of the easiest ways to generate a webpage with Clustergrammer visualizations and several of the :ref:`case_studies` are Jupyter notebooks.
+The :ref:`clustergrammer_widget` can also be used in combination with `nbviewer`_ to share static Jupyter notebook web pages with embedded interactive Clustergrammer visualizations. This is one of the easiest ways to generate a web page with Clustergrammer visualizations and several of the :ref:`case_studies` are Jupyter notebooks.
 
 .. _`nbviewer`: http://nbviewer.jupyter.org/
 .. _`homepage`: http://amp.pharm.mssm.edu/clustergrammer

diff --git a/docs/_build_html/_sources/clustergrammer_js.rst.txt b/docs/_build_html/_sources/clustergrammer_js.rst.txt
@@ -56,7 +56,7 @@ The ``id`` of the container where the visualization will be made is passed as ``
 
 Example Pages
 =============
-The `Clustergrammer GitHub repo`_ contains several example pages demonstrating how to build a webpage with a Clustergrammer visualization. The page `index.html`_ and corresponding script `load_clustergram.js`_ show how to make a full-screen resizable visualization. The page `multiple_clust.html`_ and corresponding script `load_multiple_clustergrams.js`_ show how to visualize multiple clustergrams on one page. Note that each visualization requires its own container.
+The `Clustergrammer GitHub repo`_ contains several example pages demonstrating how to build a web page with a Clustergrammer visualization. The page `index.html`_ and corresponding script `load_clustergram.js`_ show how to make a full-screen resizable visualization. The page `multiple_clust.html`_ and corresponding script `load_multiple_clustergrams.js`_ show how to visualize multiple clustergrams on one page. Note that each visualization requires its own container.
 
 .. _clustergrammer_js_api:
 

diff --git a/docs/_build_html/_sources/clustergrammer_widget.rst.txt b/docs/_build_html/_sources/clustergrammer_widget.rst.txt
@@ -112,7 +112,7 @@ The ``net`` object can also be used to filter and normalize your data before vis
 
 **Two-way Widget Communication**
 
-Jupyter widgets enable both back-end to front-end communication (e.g. Python kernel to JavaScript) and front-end to back-end (e.g. JavaScript to Python kernel). Clustergrammer-Widget uses front-end to back-end communication to enable users to export their modified matrix (e.g. cropped matrix) to the Python kernel as a DataFrame. This can be used to select a cluster of interest (e.g. by :ref:`crop` or using the :ref:`interactive_dendrogram`) and pass this cluster to a new dataframe. Alternatively, this can be used to export data to a DataFrame after running front-end enrichment analysis using :ref:`Enrichrgram <enrichrgram>`. See the ``df_widget`` method below for an example:
+Jupyter widgets enable both back-end to front-end communication (e.g. Python kernel to JavaScript) and front-end to back-end (e.g. JavaScript to Python kernel). Clustergrammer-Widget uses front-end to back-end communication to enable users to export their modified matrix (e.g. cropped matrix) to the Python kernel as a DataFrame. This can be used to select a cluster of interest (e.g. by :ref:`crop` or using the :ref:`interactive_dendrogram`) and pass this cluster to a new DataFrame. Alternatively, this can be used to export data to a DataFrame after running front-end enrichment analysis using :ref:`Enrichrgram <enrichrgram>`. See the ``df_widget`` method below for an example:
 
 ::
 
@@ -147,6 +147,8 @@ Clustergrammer-Widget's source code can be found in the `clustergrammer-widget`_
 
 Please :ref:`contact` Nicolas Fernandez and Avi Ma'ayan with questions or use the GitHub `issues`_ feature to report an issue.
 
+
+
 .. _`GitHub`: https://github.com/MaayanLab/clustergrammer-widget
 .. _`ipywidgets version 6`: https://github.com/ipython/ipywidgets/releases
 .. _`ipywidgets`: http://ipywidgets.readthedocs.io/en/latest/

diff --git a/docs/_build_html/_sources/index.rst.txt b/docs/_build_html/_sources/index.rst.txt
@@ -8,7 +8,7 @@ Clustergrammer is a web-based tool for visualizing and analyzing high-dimensiona
 
          <iframe id='iframe_preview' src="https://amp.pharm.mssm.edu/clustergrammer/demo/" frameBorder="0" style='height: 495px; width:730px; margin-bottom:20px;'></iframe>
 
-Press play or interact with the gene-expression demo below to see some of Clustergrammer's interactive features and refer to :ref:`interacting_with_viz` for more information.
+Press play or interact with the gene-expression demo above to see some of Clustergrammer's interactive features and refer to :ref:`interacting_with_viz` for more information.
 
 JupyterCon 2018
 ===============

diff --git a/docs/_build_html/app_integration.html b/docs/_build_html/app_integration.html
@@ -26,6 +26,7 @@
 
   <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+  <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="Developing Clustergrammer" href="developing_with_clustergrammer.html" />
@@ -258,6 +259,8 @@ <h2>Harmonizome<a class="headerlink" href="#harmonizome" title="Permalink to thi
         <script type="text/javascript" src="_static/jquery.js"></script>
         <script type="text/javascript" src="_static/underscore.js"></script>
         <script type="text/javascript" src="_static/doctools.js"></script>
+        <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
+        <script type="text/javascript" src="https://unpkg.com/@jupyter-widgets/html-manager@^0.14.0/dist/embed-amd.js"></script>
 
 
 

diff --git a/docs/_build_html/biology_specific_features.html b/docs/_build_html/biology_specific_features.html
@@ -26,6 +26,7 @@
 
   <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+  <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="Case Studies and Examples" href="case_studies.html" />
@@ -188,7 +189,7 @@ <h2>Enrichment Analysis<a class="headerlink" href="#enrichment-analysis" title="
 <p id="enrichrgram"><strong>Enrichrgram</strong></p>
 <p>Enrichrgram enables users to find biological information specific to their genes of interest (using <a class="reference external" href="http://amp.pharm.mssm.edu/Enrichr/">Enrichr</a>) and import this information directly into the visualization as row categories (see screenshot below). Enrichrgram can be run on the front or back end (using the <a class="reference internal" href="clustergrammer_py.html#clustergrammer-py-api"><span class="std std-ref">Clustergrammer-PY API</span></a> to pre-calculate results). This feature enables enrichment analysis to be performed within the visualization itself by both the original author of the visualization and subsequent viewers.</p>
 <p><strong>Enrichrgram Front End</strong></p>
-<p>Enrichrgram on the front end is available to anyone viewing the visualization and can be used by simply clicking the red DNA-like Enrichr logo on the top left of the heatmap, which brings up a list of Enrichr libraries to choose from. To perform enrichment analysis, choose a library and Enrichrgram will return enriched terms from this library that are specifically associated with your list of genes (P-value bars indicate the degree of specificity). For instance, clicking on <em>ChEA 2016</em> will calculate enrichment for up-stream transcription factors. The enriched terms are shown as row categoris, which enables users to see which genes are associated with each term. Row-category titles show the enriched term and the red-bars represent the significance of the enrichment (see <a class="reference external" href="http://amp.pharm.mssm.edu/Enrichr/help#basics">Enrichr combined score</a>). Users can run enrichment analysis on a specific cluster of genes by filtering the matrix to only show only their genes of interest. This filtering can be done using the Dendrogram Crop buttons (see <a class="reference internal" href="interacting_with_viz.html#interactive-dendrogram"><span class="std std-ref">Interactive Dendrogram</span></a>) or Brush-Crop button (see <a class="reference internal" href="interacting_with_viz.html#crop"><span class="std std-ref">Cropping</span></a>) to select a subset of genes for analysis.</p>
+<p>Enrichrgram on the front end is available to anyone viewing the visualization and can be used by simply clicking the red DNA-like Enrichr logo on the top left of the heatmap, which brings up a list of Enrichr libraries to choose from. To perform enrichment analysis, choose a library and Enrichrgram will return enriched terms from this library that are specifically associated with your list of genes (P-value bars indicate the degree of specificity). For instance, clicking on <em>ChEA 2016</em> will calculate enrichment for up-stream transcription factors. The enriched terms are shown as row categories, which enables users to see which genes are associated with each term. Row-category titles show the enriched term and the red-bars represent the significance of the enrichment (see <a class="reference external" href="http://amp.pharm.mssm.edu/Enrichr/help#basics">Enrichr combined score</a>). Users can run enrichment analysis on a specific cluster of genes by filtering the matrix to only show only their genes of interest. This filtering can be done using the Dendrogram Crop buttons (see <a class="reference internal" href="interacting_with_viz.html#interactive-dendrogram"><span class="std std-ref">Interactive Dendrogram</span></a>) or Brush-Crop button (see <a class="reference internal" href="interacting_with_viz.html#crop"><span class="std std-ref">Cropping</span></a>) to select a subset of genes for analysis.</p>
 <div class="figure align-left" id="id4">
 <a class="reference internal image-reference" href="_images/enrichrgram_results.png"><img alt="Enrichrgram Menu" src="_images/enrichrgram_results.png" style="width: 900px;" /></a>
 <p class="caption"><span class="caption-text">Users can perform enrichment analysis to find biological information specific to their genes (e.g. a cluster of genes). Users can select from several enrichment libraries, and the top 10 enriched terms will be shown as rows categories. The combined scores for the enriched terms will be shown as red bars behind the row category titles.</span></p>
@@ -255,6 +256,8 @@ <h2>Enrichment Analysis<a class="headerlink" href="#enrichment-analysis" title="
         <script type="text/javascript" src="_static/jquery.js"></script>
         <script type="text/javascript" src="_static/underscore.js"></script>
         <script type="text/javascript" src="_static/doctools.js"></script>
+        <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
+        <script type="text/javascript" src="https://unpkg.com/@jupyter-widgets/html-manager@^0.14.0/dist/embed-amd.js"></script>
 
 
 

diff --git a/docs/_build_html/building_webpage.html b/docs/_build_html/building_webpage.html
@@ -26,6 +26,7 @@
 
   <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+  <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="Clustergrammer-JS" href="clustergrammer_js.html" />
@@ -186,7 +187,7 @@ <h2>Adding Clustergrammer to a Page<a class="headerlink" href="#adding-clustergr
 </div>
 <div class="section" id="jupyter-notebook-webpages">
 <h2>Jupyter Notebook Webpages<a class="headerlink" href="#jupyter-notebook-webpages" title="Permalink to this headline">¶</a></h2>
-<p>The <a class="reference internal" href="clustergrammer_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer Jupyter Widget</span></a> can also be used in combination with <a class="reference external" href="http://nbviewer.jupyter.org/">nbviewer</a> to share static Jupyter notebook webpages with embedded interactive Clustergrammer visualizations. This is one of the easiest ways to generate a webpage with Clustergrammer visualizations and several of the <a class="reference internal" href="case_studies.html#case-studies"><span class="std std-ref">Case Studies and Examples</span></a> are Jupyter notebooks.</p>
+<p>The <a class="reference internal" href="clustergrammer_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer Jupyter Widget</span></a> can also be used in combination with <a class="reference external" href="http://nbviewer.jupyter.org/">nbviewer</a> to share static Jupyter notebook web pages with embedded interactive Clustergrammer visualizations. This is one of the easiest ways to generate a web page with Clustergrammer visualizations and several of the <a class="reference internal" href="case_studies.html#case-studies"><span class="std std-ref">Case Studies and Examples</span></a> are Jupyter notebooks.</p>
 </div>
 </div>
 
@@ -245,6 +246,8 @@ <h2>Jupyter Notebook Webpages<a class="headerlink" href="#jupyter-notebook-webpa
         <script type="text/javascript" src="_static/jquery.js"></script>
         <script type="text/javascript" src="_static/underscore.js"></script>
         <script type="text/javascript" src="_static/doctools.js"></script>
+        <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
+        <script type="text/javascript" src="https://unpkg.com/@jupyter-widgets/html-manager@^0.14.0/dist/embed-amd.js"></script>
 
 
 

diff --git a/docs/_build_html/case_studies.html b/docs/_build_html/case_studies.html
@@ -26,6 +26,7 @@
 
   <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+  <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" />
@@ -288,6 +289,8 @@ <h2>Single-Cell RNA-seq Data Visualization<a class="headerlink" href="#single-ce
         <script type="text/javascript" src="_static/jquery.js"></script>
         <script type="text/javascript" src="_static/underscore.js"></script>
         <script type="text/javascript" src="_static/doctools.js"></script>
+        <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
+        <script type="text/javascript" src="https://unpkg.com/@jupyter-widgets/html-manager@^0.14.0/dist/embed-amd.js"></script>