added kinase network screenshot

cornhundred · May 2, 2017 · 8127c46 · 8127c46
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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/_images/kinase_network_screenshot.png b/docs/_build_html/_images/kinase_network_screenshot.png
diff --git a/docs/_build_html/_sources/case_studies.txt b/docs/_build_html/_sources/case_studies.txt
@@ -65,6 +65,18 @@ Clustergrammer was used to visualize several widely used machine learning Datase
 
 These examples demonstrate the generality of heatmap visualizations and enable users to interactively explore familiar Datasets.
 
+Large Network: Kinase Substrate Similarity Network
+==================================================
+.. figure:: _static/kinase_network_screenshot.png
+  :width: 450px
+  :align: left
+  :alt: Kinase Network Screenshot
+  :target: https://maayanlab.github.io/kinase_substrate_similarity_network/
+
+  Screenshot from the `Kinase Substrate Similarity Network`_ example that demonstrates Clustergrammer can be used to visualize a large network of kinases based on shared substrates.
+
+Clustergrammer can be used to visualize large networks without the formation of 'hairballs'. In the `Kinase Substrate Similarity Network`_ example we use Clustergrammer to visualize a network kinases based on shared substrate that includes 404 kinases and 163,216 links. Kinases are shown as rows and columns. For more information see the `Kinase Substrate Similarity Network`_.
+
 
 Zika Virus RNA-seq Data Visualization
 =====================================
@@ -75,7 +87,7 @@ Single-Cell RNA-seq Data Visualization
 Clustergrammer was used to visualize published single-cell gene expression data: `Single-Cell RNA-seq Data Visualization`_ (`Olsson et al.`_). The visualization was produced using an Excel file provided alongside the figures.
 
 
-
+.. _`Kinase Substrate Similarity Network`: https://maayanlab.github.io/kinase_substrate_similarity_network/
 .. _`MNIST Data`: http://yann.lecun.com/exdb/mnist/
 .. _`Icahn School of Medicine Human Immune Monitoring Core`: http://icahn.mssm.edu/research/portal/resources/deans-cores/human-immune-monitoring-core
 .. _`Plasma_vs_PMA_Phosphrylation.ipynb`: http://nbviewer.jupyter.org/github/MaayanLab/Cytof_Plasma_PMA/blob/master/notebooks/Plasma_vs_PMA_Phosphorylation.ipynb

diff --git a/docs/_build_html/_static/kinase_network_screenshot.png b/docs/_build_html/_static/kinase_network_screenshot.png
diff --git a/docs/_build_html/case_studies.html b/docs/_build_html/case_studies.html
@@ -94,6 +94,7 @@
 <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>
 <li class="toctree-l2"><a class="reference internal" href="#machine-learning-and-miscellaneous-datasets">Machine Learning and Miscellaneous Datasets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#large-network-kinase-substrate-similarity-network">Large Network: Kinase Substrate Similarity Network</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#zika-virus-rna-seq-data-visualization">Zika Virus RNA-seq Data Visualization</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#single-cell-rna-seq-data-visualization">Single-Cell RNA-seq Data Visualization</a></li>
 </ul>
@@ -195,6 +196,14 @@ <h2>Machine Learning and Miscellaneous Datasets<a class="headerlink" href="#mach
 </ul>
 <p>These examples demonstrate the generality of heatmap visualizations and enable users to interactively explore familiar Datasets.</p>
 </div>
+<div class="section" id="large-network-kinase-substrate-similarity-network">
+<h2>Large Network: Kinase Substrate Similarity Network<a class="headerlink" href="#large-network-kinase-substrate-similarity-network" title="Permalink to this headline">¶</a></h2>
+<div class="figure align-left" id="id6">
+<a class="reference external image-reference" href="https://maayanlab.github.io/kinase_substrate_similarity_network/"><img alt="Kinase Network Screenshot" src="_images/kinase_network_screenshot.png" style="width: 450px;" /></a>
+<p class="caption"><span class="caption-text">Screenshot from the <a class="reference external" href="https://maayanlab.github.io/kinase_substrate_similarity_network/">Kinase Substrate Similarity Network</a> example that demonstrates Clustergrammer can be used to visualize a large network of kinases based on shared substrates.</span></p>
+</div>
+<p>Clustergrammer can be used to visualize large networks without the formation of &#8216;hairballs&#8217;. In the <a class="reference external" href="https://maayanlab.github.io/kinase_substrate_similarity_network/">Kinase Substrate Similarity Network</a> example we use Clustergrammer to visualize a network kinases based on shared substrate that includes 404 kinases and 163,216 links. Kinases are shown as rows and columns. For more information see the <a class="reference external" href="https://maayanlab.github.io/kinase_substrate_similarity_network/">Kinase Substrate Similarity Network</a>.</p>
+</div>
 <div class="section" id="zika-virus-rna-seq-data-visualization">
 <h2>Zika Virus RNA-seq Data Visualization<a class="headerlink" href="#zika-virus-rna-seq-data-visualization" title="Permalink to this headline">¶</a></h2>
 <p>Clustergrammer was used to visualize the results of an RNA-Seq data analysis pipeline within a Jupyter notebook: <a class="reference external" href="http://nbviewer.jupyter.org/github/maayanlab/Zika-RNAseq-Pipeline/blob/master/Zika.ipynb">An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study</a> (<a class="reference external" href="https://f1000research.com/articles/5-1574/v1">Wang et al.</a>).</p>

diff --git a/docs/_build_html/index.html b/docs/_build_html/index.html
@@ -230,6 +230,7 @@ <h2>Contents:<a class="headerlink" href="#contents" title="Permalink to this hea
 <li class="toctree-l2"><a class="reference internal" href="case_studies.html#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="case_studies.html#cytof-data-single-cell-immune-response-to-pma-treatment">CyTOF Data: Single Cell Immune Response to PMA Treatment</a></li>
 <li class="toctree-l2"><a class="reference internal" href="case_studies.html#machine-learning-and-miscellaneous-datasets">Machine Learning and Miscellaneous Datasets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="case_studies.html#large-network-kinase-substrate-similarity-network">Large Network: Kinase Substrate Similarity Network</a></li>
 <li class="toctree-l2"><a class="reference internal" href="case_studies.html#zika-virus-rna-seq-data-visualization">Zika Virus RNA-seq Data Visualization</a></li>
 <li class="toctree-l2"><a class="reference internal" href="case_studies.html#single-cell-rna-seq-data-visualization">Single-Cell RNA-seq Data Visualization</a></li>
 </ul>

diff --git a/docs/_build_html/searchindex.js b/docs/_build_html/searchindex.js
diff --git a/docs/_static/kinase_network_screenshot.png b/docs/_static/kinase_network_screenshot.png
diff --git a/docs/case_studies.rst b/docs/case_studies.rst
@@ -65,6 +65,18 @@ Clustergrammer was used to visualize several widely used machine learning Datase
 
 These examples demonstrate the generality of heatmap visualizations and enable users to interactively explore familiar Datasets.
 
+Large Network: Kinase Substrate Similarity Network
+==================================================
+.. figure:: _static/kinase_network_screenshot.png
+  :width: 450px
+  :align: left
+  :alt: Kinase Network Screenshot
+  :target: https://maayanlab.github.io/kinase_substrate_similarity_network/
+
+  Screenshot from the `Kinase Substrate Similarity Network`_ example that demonstrates Clustergrammer can be used to visualize a large network of kinases based on shared substrates.
+
+Clustergrammer can be used to visualize large networks without the formation of 'hairballs'. In the `Kinase Substrate Similarity Network`_ example we use Clustergrammer to visualize a network kinases based on shared substrate that includes 404 kinases and 163,216 links. Kinases are shown as rows and columns. For more information see the `Kinase Substrate Similarity Network`_.
+
 
 Zika Virus RNA-seq Data Visualization
 =====================================
@@ -75,7 +87,7 @@ Single-Cell RNA-seq Data Visualization
 Clustergrammer was used to visualize published single-cell gene expression data: `Single-Cell RNA-seq Data Visualization`_ (`Olsson et al.`_). The visualization was produced using an Excel file provided alongside the figures.
 
 
-
+.. _`Kinase Substrate Similarity Network`: https://maayanlab.github.io/kinase_substrate_similarity_network/
 .. _`MNIST Data`: http://yann.lecun.com/exdb/mnist/
 .. _`Icahn School of Medicine Human Immune Monitoring Core`: http://icahn.mssm.edu/research/portal/resources/deans-cores/human-immune-monitoring-core
 .. _`Plasma_vs_PMA_Phosphrylation.ipynb`: http://nbviewer.jupyter.org/github/MaayanLab/Cytof_Plasma_PMA/blob/master/notebooks/Plasma_vs_PMA_Phosphorylation.ipynb