built with spelling changes

docs/_build_html/_sources/biology_specific_features.txt

@@ -6,15 +6,15 @@ Clustergrammer was built to visualize high-dimensional biological data (e.g. gen
 
 Mouseover Gene Name and Description
 ===================================
-The human genome consists of over 20,000 genes and modern high-throughput measurements are capable of making measurements across the entire genome (e.g. genome-wide expression studies). Human genes have official gene symbols (e.g. EGFR) that are frequently used to label genes in these datasets. Since no biologist can be knowledgable about every gene in the genome a common and repetitive task for biologists is looking up the names and descriptions of genes (given as official gene symbols) in a dataset or visualization. To streamline this, Clustergrammer automatically gives the full name and description of a gene (provided by data aggregated through the `Harmonizome`_) as a tooltip when a user mouses over a gene label. This simple feature speeds up analysis of large gene-level datasets.
+The human genome consists of over 20,000 genes and modern high-throughput measurements are capable of making measurements across the entire genome (e.g. genome-wide expression studies). Human genes have official gene symbols (e.g. EGFR) that are frequently used to label genes in these datasets. Since no biologist can be knowledgeable about every gene in the genome a common and repetitive task for biologists is looking up the names and descriptions of genes (given as official gene symbols) in a dataset or visualization. To streamline this, Clustergrammer automatically gives the full name and description of a gene (provided by data aggregated through the `Harmonizome`_) as a tooltip when a user mouses over a gene label. This simple feature speeds up analysis of large gene-level datasets.
 
 The JavaScript file `hzome_functions.js`_ provides this functionality by utilizing `Harmonizome's RESTful API`_ to obtain gene names and descriptions on mouseover events. `hzome_functions.js`_ is passed to :ref:`clustergrammer_js` as a callback function. See `load_clustergram.js`_ for an example use case. This method of enhancing :ref:`clustergrammer_js`'s behavior can be extended by developers for other use cases.
 
 Enrichment Analysis
 ===================
 The field of biology has amassed an enormous amount of information about the genes in living organisms such as: function, disease-association, up-stream regulators, protein-level binding partners, etc. Integration of this information can help biologists understand patterns in their data. For instance, enrichment analysis a popular method to identify biological information specific to a list of genes - e.g. a biologist may use enrichment analysis to identify up-stream regulatory transcription factors that specifically target their measured set of up-regulated genes and thereby form hypotheses about potential up-stream regulators in their system.
 
-When a user visualizes a matrix with genes as rows, Clustergrammer automatically enables intergration with the enrichment analysis tool `Enrichr`_. Users can export their genes of interest to Enrichr using the interactive dendrogram or import enrichment results from Enrichr using the Enrichr tool on the top left.
+When a user visualizes a matrix with genes as rows, Clustergrammer automatically enables integration with the enrichment analysis tool `Enrichr`_. Users can export their genes of interest to Enrichr using the interactive dendrogram or import enrichment results from Enrichr using the Enrichr tool on the top left.
 
 The JavaScript file `Enrichrgram.js`_ provides this functionality using `Enrichr's RESTful API`_ to generate enrichment results from a list of input genes. `Enrichrgram.js`_ works with the :ref:`clustergrammer_js` API to depict enriched terms and their associated genes as row categories by adding/removing row categories. This general behavior of adding/removing row categories can be extended by developers for other use cases.
 

docs/_build_html/_sources/building_webpage.txt

@@ -12,7 +12,7 @@ The Clustergrammer web app can be used to produce visualizations that are embedd
 
   <iframe id="iframe_preview" src="http://amp.pharm.mssm.edu/clustergrammer/viz/5734a7399fee36034aeb787e/rc_two_cats.txt" frameborder="0"></iframe>
 
-Users can obtain a permanent link to their visualization by manually uploading their data  using the upload section of Clustergrammer-Web's `homepage`_ and copying the URL to the full-screen version of their visualization. Alternatively users can programatically upload their data using the :ref:`clustergrammer_web_api` and receive their permanent links through the API.
+Users can obtain a permanent link to their visualization by manually uploading their data  using the upload section of Clustergrammer-Web's `homepage`_ and copying the URL to the full-screen version of their visualization. Alternatively users can programmatically upload their data using the :ref:`clustergrammer_web_api` and receive their permanent links through the API.
 
 
 Adding Clustergrammer to a Page

docs/_build_html/_sources/clustergrammer_js.txt

@@ -22,7 +22,7 @@ Clustergrammer.js can be installed using node package manager (`npm package`_) w
 
   npm install clustergrammer
 
-or the source code and library, ``clustergrammer.js``, can be obtained from the `clustergrammer`_ Github repo.
+or the source code and library, ``clustergrammer.js``, can be obtained from the `clustergrammer`_ GitHub repo.
 
 .. _javascript_workflow_example:
 
@@ -39,13 +39,13 @@ This workflow shows how to make a visualization using a JSON produced by Cluster
 
   var cgm = Clustergrammer(args);
 
-The id of the container where the visualizaton will be made is passed as ``root`` (this root container must be made by the user). The visualization JSON contains the information necessary to make the visualization and is passed as ``network_data``. See the Clustergrammer.js API for additional arguments that can be passed to Clustergrammer.js.
+The id of the container where the visualization will be made is passed as ``root`` (this root container must be made by the user). The visualization JSON contains the information necessary to make the visualization and is passed as ``network_data``. See the Clustergrammer.js API for additional arguments that can be passed to Clustergrammer.js.
 
 .. _example_pages:
 
 Example Pages
 =============
-The `clustergrammer`_ contains several example pages demonstrating how to make a webpage with a Clustergramemr heatmap. The page `index.html`_ and corresponding script `load_clustergram.js`_ show how to make a full-screen resizable visualization.
+The `clustergrammer`_ contains several example pages demonstrating how to make a webpage with a Clustergrammer heatmap. 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 heatmap requires its own container.
 

docs/_build_html/_sources/clustergrammer_py.txt

@@ -4,7 +4,7 @@ Clustergrammer-PY
 -----------------
 |pypi-version|
 
-Clustergrammer-PY is the back-end Python library that is used to hierarchically cluster the data and generate the JSON for the front-end Clustergrammer.js visualization library. Clustergramer-PY is compatable with Python 2 and 3.
+Clustergrammer-PY is the back-end Python library that is used to hierarchically cluster the data and generate the JSON for the front-end Clustergrammer.js visualization library. Clustergrammer-PY is compatible with Python 2 and 3.
 
 Dependencies
 ============

docs/_build_html/_sources/clustergrammer_web.txt

@@ -28,7 +28,7 @@ Uploading a matrix to Clustergrammer-Web will redirect the user to a new permane
 
 Clustergrammer-Web API
 ======================
-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.
+Clustergrammer-Web's RESful API enables users to programmatically 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.
 
 *Matrix Upload*
 

docs/_build_html/_sources/clustergrammer_widget.txt

@@ -5,7 +5,7 @@ Clustergrammer Jupyter Widget
 |pypi-version|
 |npm-version|
 
-Clustergrammer can be used within a Jupyter notebook as an interactive HTML widget and is compatable with Python 2 and 3. Clustergrammer-Widget can be used to visualize a matrix of data from a file or from a `Pandas`_ DataFrame.
+Clustergrammer can be used within a Jupyter notebook as an interactive HTML widget and is compatible with Python 2 and 3. Clustergrammer-Widget can be used to visualize a matrix of data from a file or from a `Pandas`_ DataFrame.
 
 
 Dependencies

docs/_build_html/_sources/index.txt

@@ -16,7 +16,7 @@ The easiest ways to use Clustergrammer to produce an interactive and shareable h
 - upload a tab-separated matrix file using the Clustergrammer web app `homepage`_
 - or use the :ref:`clustergrammer_widget` within a `Jupyter`_ notebook and share with `nbviewer`_
 
-The :ref:`clustergrammer_web` is the quickest way for a user to generate an interactive and shareable visualization (see `example visualization`_). For more technical users, the :ref:`clustergrammer_widget` enables visualizations to be built within Jupyter notebook workflows and shared through Jupyter's `nbviewer`_ (see `example notebook`_). Web developers can use Clustergrammer's core libraries (:ref:`clustergrammer_js` and :ref:`clustergrammer_py`) or the :ref:`clustergrammer_web_api` to dynamically generate visualizations for their own web appliications (see examples in :ref:`app_integration`).
+The :ref:`clustergrammer_web` is the quickest way for a user to generate an interactive and shareable visualization (see `example visualization`_). For more technical users, the :ref:`clustergrammer_widget` enables visualizations to be built within Jupyter notebook workflows and shared through Jupyter's `nbviewer`_ (see `example notebook`_). Web developers can use Clustergrammer's core libraries (:ref:`clustergrammer_js` and :ref:`clustergrammer_py`) or the :ref:`clustergrammer_web_api` to dynamically generate visualizations for their own web applications (see examples in :ref:`app_integration`).
 
 Please read the :doc:`getting_started` guide for more detailed information on using Clustergrammer.
 

docs/_build_html/_sources/license.txt

@@ -3,7 +3,7 @@ License
 
 Clustergrammer was developed by Nicolas F. Fernandez in the `Ma'ayan lab`_ at the `Icahn School of Medicine at Mount Sinai`_.
 
-Clustergrammer's `license`_ and thrid-party licenses are in the `LICENSES`_ directory.
+Clustergrammer's `license`_ and third-party licenses are in the `LICENSES`_ directory.
 
 .. _`Ma'ayan lab`: http://labs.icahn.mssm.edu/maayanlab/
 .. _`Icahn School of Medicine at Mount Sinai`: http://icahn.mssm.edu/

docs/_build_html/_sources/matrix_format_io.txt

@@ -26,7 +26,7 @@ Row and column categories can also be included in the matrix in the following wa
 .. image:: _static/cat_tsv.png
 	:width: 700px
 
-This screenshot of an Excel spreadsheet shows a single row category being added as an additional column of strings (e.g. ``Type: Interesting``) and a single column category being added as an additional row of strings (e.g. ``Gender: Male``). Up to 15 categories can be added in a similar manner. Titles for row or column names or categories can be added by prefixing each string with ``'Title: '`` (note that a space after the colon). For example the title of the column names is ``Cell Line`` and the title of the row categories is ``Gender``. See `rc_two_cats.txt`_ for an exmaple of this matrix format.
+This screenshot of an Excel spreadsheet shows a single row category being added as an additional column of strings (e.g. ``Type: Interesting``) and a single column category being added as an additional row of strings (e.g. ``Gender: Male``). Up to 15 categories can be added in a similar manner. Titles for row or column names or categories can be added by prefixing each string with ``'Title: '`` (note that a space after the colon). For example the title of the column names is ``Cell Line`` and the title of the row categories is ``Gender``. See `rc_two_cats.txt`_ for an example of this matrix format.
 
 Tuple Matrix-Category Format
 ============================

docs/_build_html/biology_specific_features.html

@@ -148,13 +148,13 @@
 <p>Clustergrammer was built to visualize high-dimensional biological data (e.g. genome-wide expression data), but can be generally applied to any high-dimensional data (e.g. any matrix). Clustergrammer has several biology-specific features that facilitate analysis of gene-level biological data, such as: gene-expression data, proteomics-data, etc. To take advantage of these features gene-level data (e.g. dimensions) must be given as rows. See <a class="reference external" href="http://amp.pharm.mssm.edu/clustergrammer/CCLE/">CCLE Explorer</a> for examples of gene-expression data. These features are available in the <a class="reference internal" href="clustergrammer_web.html#clustergrammer-web"><span class="std std-ref">Clustergrammer Web App</span></a> as well as the <a class="reference internal" href="clustergrammer_widget.html#clustergrammer-widget"><span class="std std-ref">Clustergrammer Jupyter Widget</span></a>.</p>
 <div class="section" id="mouseover-gene-name-and-description">
 <h2>Mouseover Gene Name and Description<a class="headerlink" href="#mouseover-gene-name-and-description" title="Permalink to this headline">¶</a></h2>
-<p>The human genome consists of over 20,000 genes and modern high-throughput measurements are capable of making measurements across the entire genome (e.g. genome-wide expression studies). Human genes have official gene symbols (e.g. EGFR) that are frequently used to label genes in these datasets. Since no biologist can be knowledgable about every gene in the genome a common and repetitive task for biologists is looking up the names and descriptions of genes (given as official gene symbols) in a dataset or visualization. To streamline this, Clustergrammer automatically gives the full name and description of a gene (provided by data aggregated through the <a class="reference external" href="http://amp.pharm.mssm.edu/Harmonizome/">Harmonizome</a>) as a tooltip when a user mouses over a gene label. This simple feature speeds up analysis of large gene-level datasets.</p>
+<p>The human genome consists of over 20,000 genes and modern high-throughput measurements are capable of making measurements across the entire genome (e.g. genome-wide expression studies). Human genes have official gene symbols (e.g. EGFR) that are frequently used to label genes in these datasets. Since no biologist can be knowledgeable about every gene in the genome a common and repetitive task for biologists is looking up the names and descriptions of genes (given as official gene symbols) in a dataset or visualization. To streamline this, Clustergrammer automatically gives the full name and description of a gene (provided by data aggregated through the <a class="reference external" href="http://amp.pharm.mssm.edu/Harmonizome/">Harmonizome</a>) as a tooltip when a user mouses over a gene label. This simple feature speeds up analysis of large gene-level datasets.</p>
 <p>The JavaScript file <a class="reference external" href="https://github.com/MaayanLab/clustergrammer/blob/master/js/hzome_functions.js">hzome_functions.js</a> provides this functionality by utilizing <a class="reference external" href="http://amp.pharm.mssm.edu/Harmonizome/documentation">Harmonizome&#8217;s RESTful API</a> to obtain gene names and descriptions on mouseover events. <a class="reference external" href="https://github.com/MaayanLab/clustergrammer/blob/master/js/hzome_functions.js">hzome_functions.js</a> is passed to <a class="reference internal" href="clustergrammer_js.html#clustergrammer-js"><span class="std std-ref">Clustergrammer-JS</span></a> as a callback function. See <a class="reference external" href="https://github.com/MaayanLab/clustergrammer/blob/master/js/load_clustergram.js">load_clustergram.js</a> for an example use case. This method of enhancing <a class="reference internal" href="clustergrammer_js.html#clustergrammer-js"><span class="std std-ref">Clustergrammer-JS</span></a>&#8216;s behavior can be extended by developers for other use cases.</p>
 </div>
 <div class="section" id="enrichment-analysis">
 <h2>Enrichment Analysis<a class="headerlink" href="#enrichment-analysis" title="Permalink to this headline">¶</a></h2>
 <p>The field of biology has amassed an enormous amount of information about the genes in living organisms such as: function, disease-association, up-stream regulators, protein-level binding partners, etc. Integration of this information can help biologists understand patterns in their data. For instance, enrichment analysis a popular method to identify biological information specific to a list of genes - e.g. a biologist may use enrichment analysis to identify up-stream regulatory transcription factors that specifically target their measured set of up-regulated genes and thereby form hypotheses about potential up-stream regulators in their system.</p>
-<p>When a user visualizes a matrix with genes as rows, Clustergrammer automatically enables intergration with the enrichment analysis tool <a class="reference external" href="http://amp.pharm.mssm.edu/Enrichr/">Enrichr</a>. Users can export their genes of interest to Enrichr using the interactive dendrogram or import enrichment results from Enrichr using the Enrichr tool on the top left.</p>
+<p>When a user visualizes a matrix with genes as rows, Clustergrammer automatically enables integration with the enrichment analysis tool <a class="reference external" href="http://amp.pharm.mssm.edu/Enrichr/">Enrichr</a>. Users can export their genes of interest to Enrichr using the interactive dendrogram or import enrichment results from Enrichr using the Enrichr tool on the top left.</p>
 <p>The JavaScript file <a class="reference external" href="https://github.com/MaayanLab/clustergrammer/blob/master/js/Enrichrgram.js">Enrichrgram.js</a> provides this functionality using <a class="reference external" href="http://amp.pharm.mssm.edu/Enrichr/help#api">Enrichr&#8217;s RESTful API</a> to generate enrichment results from a list of input genes. <a class="reference external" href="https://github.com/MaayanLab/clustergrammer/blob/master/js/Enrichrgram.js">Enrichrgram.js</a> works with the <a class="reference internal" href="clustergrammer_js.html#clustergrammer-js"><span class="std std-ref">Clustergrammer-JS</span></a> API to depict enriched terms and their associated genes as row categories by adding/removing row categories. This general behavior of adding/removing row categories can be extended by developers for other use cases.</p>
 </div>
 </div>