added internal short-name links in interacting_with_viz

docs/_build_html/_sources/interacting_with_viz.txt

@@ -31,6 +31,19 @@ Mousing over visualization elements brings up more information in tooltips. For
 
 See :ref:`clustergrammer_js_api` for information about adding callback functions to mouseover events and :ref:`hzome_gene_info` for biology specific mouseover behavior.
 
+.. _sidebar_interactions:
+
+Sidebar Interactions
+====================
+Clustergrammer visualizations have a sidebar section that contains:
+
+- optional about section (see :ref:`clustergrammer_js_api`)
+- icon buttons: share_, snapshot_, download_, cropping_
+- row and column reordering buttons
+- row search box
+- opacity slider
+- row-filter-sliders
+
 .. _row_col_reordering:
 
 Row and Column Reordering
@@ -81,20 +94,33 @@ Interactive Categories
 
 *category updating API*
 
+.. _cropping:
+
 Cropping
 ========
 *brush cropping*
 
+.. _download:
+
 Downloading Data from the Visualization
 =======================================
 Obtaining the underlying data from a visualization for re-use and re-analysis can be a tedious task. To facilitate this common task, Clustergrammer's sidebar has a download icon, shown below, that allows users to download the matrix of data in the visualization. The downloaded data reflects the current state of the matrix, e.g. filtering, cropping, and reordering will be reflected in the downloaded data.
 
   **<screenshot of download button in sidebar>**
 
+.. _snapshot:
+
 Taking a Snapshot of the Visualization
 ======================================
 *stateful snapshots of matrix*
 
+.. _share_heatmap:
+.. _share:
+
+Sharing your Interactive Heatmap
+================================
+Interactive heatmaps produced with the :ref:`clustergrammer_web` and the :ref:`clustergrammer_widget` (when notebooks are rendered through `nbviewer`_) can easily be shared with collaborators by sharing the URL of the visualization on the web app or the notebook. Users can also click the share button on the sidebar (see :ref:`sidebar_interactions`) sidebar to get this shareable URL.
+
 Changing the Opacity
 ====================
 *useful for dealing with outlier values*
@@ -109,11 +135,12 @@ Expanding
 
 Biology Specific Interactions
 =============================
-**
+
 
 .. _`Eisen et al., 1998`: http://www.pnas.org/content/95/25/14863.full
 .. _`dendrogram trees`: https://en.wikipedia.org/wiki/Dendrogram
 .. _`t-SNE`: https://lvdmaaten.github.io/tsne/
 .. _`hierarchical clustering`: https://docs.scipy.org/doc/scipy-0.18.1/reference/cluster.hierarchy.html
 .. _`PCA`: https://en.wikipedia.org/wiki/Principal_component_analysis
-.. _`object constancy`: https://bost.ocks.org/mike/constancy/
+.. _`object constancy`: https://bost.ocks.org/mike/constancy/
+.. _`nbviewer`: http://nbviewer.jupyter.org/

docs/_build_html/index.html

@@ -194,13 +194,15 @@ <h2>Contents:<a class="headerlink" href="#contents" title="Permalink to this hea
 <li class="toctree-l2"><a class="reference internal" href="interacting_with_viz.html#introduction-to-clustergrams-heatmaps">Introduction to Clustergrams/Heatmaps</a></li>
 <li class="toctree-l2"><a class="reference internal" href="interacting_with_viz.html#zooming-and-panning">Zooming and Panning</a></li>
 <li class="toctree-l2"><a class="reference internal" href="interacting_with_viz.html#mouseover-interactions">Mouseover Interactions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="interacting_with_viz.html#sidebar-interactions">Sidebar Interactions</a></li>
 <li class="toctree-l2"><a class="reference internal" href="interacting_with_viz.html#row-and-column-reordering">Row and Column Reordering</a></li>
 <li class="toctree-l2"><a class="reference internal" href="interacting_with_viz.html#interactive-dimensionality-reduction">Interactive Dimensionality Reduction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="interacting_with_viz.html#interactive-dendrogram">Interactive Dendrogram</a></li>
 <li class="toctree-l2"><a class="reference internal" href="interacting_with_viz.html#interactive-categories">Interactive Categories</a></li>
 <li class="toctree-l2"><a class="reference internal" href="interacting_with_viz.html#cropping">Cropping</a></li>
 <li class="toctree-l2"><a class="reference internal" href="interacting_with_viz.html#downloading-data-from-the-visualization">Downloading Data from the Visualization</a></li>
 <li class="toctree-l2"><a class="reference internal" href="interacting_with_viz.html#taking-a-snapshot-of-the-visualization">Taking a Snapshot of the Visualization</a></li>
+<li class="toctree-l2"><a class="reference internal" href="interacting_with_viz.html#sharing-your-interactive-heatmap">Sharing your Interactive Heatmap</a></li>
 <li class="toctree-l2"><a class="reference internal" href="interacting_with_viz.html#changing-the-opacity">Changing the Opacity</a></li>
 <li class="toctree-l2"><a class="reference internal" href="interacting_with_viz.html#row-searching">Row Searching</a></li>
 <li class="toctree-l2"><a class="reference internal" href="interacting_with_viz.html#expanding">Expanding</a></li>

docs/_build_html/interacting_with_viz.html

@@ -89,13 +89,15 @@
 <li class="toctree-l2"><a class="reference internal" href="#introduction-to-clustergrams-heatmaps">Introduction to Clustergrams/Heatmaps</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#zooming-and-panning">Zooming and Panning</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#mouseover-interactions">Mouseover Interactions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#sidebar-interactions">Sidebar Interactions</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#row-and-column-reordering">Row and Column Reordering</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#interactive-dimensionality-reduction">Interactive Dimensionality Reduction</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#interactive-dendrogram">Interactive Dendrogram</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#interactive-categories">Interactive Categories</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#cropping">Cropping</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#downloading-data-from-the-visualization">Downloading Data from the Visualization</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#taking-a-snapshot-of-the-visualization">Taking a Snapshot of the Visualization</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#sharing-your-interactive-heatmap">Sharing your Interactive Heatmap</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#changing-the-opacity">Changing the Opacity</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#row-searching">Row Searching</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#expanding">Expanding</a></li>
@@ -178,6 +180,18 @@ <h2>Mouseover Interactions<a class="headerlink" href="#mouseover-interactions" t
 <div><strong>&lt;screenshot of mouseover tooltip&gt;</strong></div></blockquote>
 <p>See <a class="reference internal" href="clustergrammer_js.html#clustergrammer-js-api"><span class="std std-ref">Clustergrammer-JS API</span></a> for information about adding callback functions to mouseover events and <a class="reference internal" href="biology_specific_features.html#hzome-gene-info"><span class="std std-ref">Mouseover Gene Name and Description</span></a> for biology specific mouseover behavior.</p>
 </div>
+<div class="section" id="sidebar-interactions">
+<span id="id1"></span><h2>Sidebar Interactions<a class="headerlink" href="#sidebar-interactions" title="Permalink to this headline">¶</a></h2>
+<p>Clustergrammer visualizations have a sidebar section that contains:</p>
+<ul class="simple">
+<li>optional about section (see <a class="reference internal" href="clustergrammer_js.html#clustergrammer-js-api"><span class="std std-ref">Clustergrammer-JS API</span></a>)</li>
+<li>icon buttons: <a class="reference internal" href="#share">share</a>, <a class="reference internal" href="#snapshot">snapshot</a>, <a class="reference internal" href="#download">download</a>, <a class="reference internal" href="#cropping">cropping</a></li>
+<li>row and column reordering buttons</li>
+<li>row search box</li>
+<li>opacity slider</li>
+<li>row-filter-sliders</li>
+</ul>
+</div>
 <div class="section" id="row-and-column-reordering">
 <span id="row-col-reordering"></span><h2>Row and Column Reordering<a class="headerlink" href="#row-and-column-reordering" title="Permalink to this headline">¶</a></h2>
 <p>Clustergrammer allows users to order rows and columns based on:</p>
@@ -199,32 +213,36 @@ <h2>Mouseover Interactions<a class="headerlink" href="#mouseover-interactions" t
 <p>For small matrices dimensionality reduction is animated to help the user visualize the effects this transformation. Clustergrammer employs the concept of <a class="reference external" href="https://bost.ocks.org/mike/constancy/">object constancy</a> by using animations to help the user visually follow changes to their data. Filtering out dimensions (rows) occurs in two steps: 1) filtered rows fade out, then the remaining rows rearrange themselves into their new order (e.g. clustering order). Adding back in dimensions (rows) occurs in two steps: the current rows rearrange themselves into their new positions, then the new rows fade into view.</p>
 </div>
 <div class="section" id="interactive-dendrogram">
-<span id="id1"></span><h2>Interactive Dendrogram<a class="headerlink" href="#interactive-dendrogram" title="Permalink to this headline">¶</a></h2>
+<span id="id2"></span><h2>Interactive Dendrogram<a class="headerlink" href="#interactive-dendrogram" title="Permalink to this headline">¶</a></h2>
 <p><em>explain what a dendrogram is</em></p>
 <p><em>explain how a user can interact with the dendrogram</em></p>
 <p><em>explain how a user can crop using the dendrogram</em></p>
 </div>
 <div class="section" id="interactive-categories">
-<span id="id2"></span><h2>Interactive Categories<a class="headerlink" href="#interactive-categories" title="Permalink to this headline">¶</a></h2>
+<span id="id3"></span><h2>Interactive Categories<a class="headerlink" href="#interactive-categories" title="Permalink to this headline">¶</a></h2>
 <p><em>Explain why categories are useful</em></p>
 <p><em>mouseover highlighting, reordering, dendrogram breakdown</em></p>
 <p><em>category types: string value</em></p>
 <p><em>category updating API</em></p>
 </div>
 <div class="section" id="cropping">
-<h2>Cropping<a class="headerlink" href="#cropping" title="Permalink to this headline">¶</a></h2>
+<span id="id4"></span><h2>Cropping<a class="headerlink" href="#cropping" title="Permalink to this headline">¶</a></h2>
 <p><em>brush cropping</em></p>
 </div>
 <div class="section" id="downloading-data-from-the-visualization">
-<h2>Downloading Data from the Visualization<a class="headerlink" href="#downloading-data-from-the-visualization" title="Permalink to this headline">¶</a></h2>
+<span id="download"></span><h2>Downloading Data from the Visualization<a class="headerlink" href="#downloading-data-from-the-visualization" title="Permalink to this headline">¶</a></h2>
 <p>Obtaining the underlying data from a visualization for re-use and re-analysis can be a tedious task. To facilitate this common task, Clustergrammer&#8217;s sidebar has a download icon, shown below, that allows users to download the matrix of data in the visualization. The downloaded data reflects the current state of the matrix, e.g. filtering, cropping, and reordering will be reflected in the downloaded data.</p>
 <blockquote>
 <div><strong>&lt;screenshot of download button in sidebar&gt;</strong></div></blockquote>
 </div>
 <div class="section" id="taking-a-snapshot-of-the-visualization">
-<h2>Taking a Snapshot of the Visualization<a class="headerlink" href="#taking-a-snapshot-of-the-visualization" title="Permalink to this headline">¶</a></h2>
+<span id="snapshot"></span><h2>Taking a Snapshot of the Visualization<a class="headerlink" href="#taking-a-snapshot-of-the-visualization" title="Permalink to this headline">¶</a></h2>
 <p><em>stateful snapshots of matrix</em></p>
 </div>
+<div class="section" id="sharing-your-interactive-heatmap">
+<span id="share"></span><span id="share-heatmap"></span><h2>Sharing your Interactive Heatmap<a class="headerlink" href="#sharing-your-interactive-heatmap" title="Permalink to this headline">¶</a></h2>
+<p>Interactive heatmaps produced with 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 Jupyter Widget</span></a> (when notebooks are rendered through <a class="reference external" href="http://nbviewer.jupyter.org/">nbviewer</a>) can easily be shared with collaborators by sharing the URL of the visualization on the web app or the notebook. Users can also click the share button on the sidebar (see <a class="reference internal" href="#sidebar-interactions"><span class="std std-ref">Sidebar Interactions</span></a>) sidebar to get this shareable URL.</p>
+</div>
 <div class="section" id="changing-the-opacity">
 <h2>Changing the Opacity<a class="headerlink" href="#changing-the-opacity" title="Permalink to this headline">¶</a></h2>
 <p><em>useful for dealing with outlier values</em></p>
@@ -239,7 +257,6 @@ <h2>Expanding<a class="headerlink" href="#expanding" title="Permalink to this he
 </div>
 <div class="section" id="biology-specific-interactions">
 <h2>Biology Specific Interactions<a class="headerlink" href="#biology-specific-interactions" title="Permalink to this headline">¶</a></h2>
-<p><a href="#id3"><span class="problematic" id="id4">**</span></a></p>
 </div>
 </div>