Added line breaks and formatting updates.

serrano-pozo-lab · Jul 27, 2021 · d40a5d6 · d40a5d6
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diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@ We performed a systematic review of the neuropathological literature followed by
 
 ## Dependencies
 
-To run our code, please install the [R](https://www.r-project.org/) programming language and statistical computing environment (version 4.1.0). Additional required libraries are specified in each script.
+To run our code, please install the [R](https://www.r-project.org/) programming language and statistical computing environment (version 4.1.0). Additional required packages are specified in each script.
 
 <a href="https://www.r-project.org/" target="_blank" rel="noreferrer noopener"><img src="https://img.shields.io/badge/Language-R-276DC3?style=for-the-badge&amp;logo=r" alt="ayushnoori" align="center"/></a>
 

diff --git a/docs/404.html b/docs/404.html
@@ -1911,6 +1911,7 @@
     --text-color:      rgba(0, 0, 0, 0.5);
   }
 
+
   /*-- WEBSITE HEADER + FOOTER --*/
   /* These properties only apply to Distill sites and blogs  */
 
@@ -1926,7 +1927,7 @@
     --text-color:       rgba(255, 255, 255, 0.8);
     --text-size:        15px;
     --hover-color:      white;
-    --bkgd-color:       #7D451B;
+    --bkgd-color:       #999999;
   }
 
   /*-- Additional custom styles --*/
@@ -1961,7 +1962,7 @@
   h1 {
     margin-top: 2em !important;
     font-size: 36px !important;
-    color: #7D451B !important;
+    color: #7F5539 !important;
   }
 
   d-article h1:nth-child(2) {

diff --git a/docs/index.html b/docs/index.html
@@ -1914,6 +1914,7 @@
     --text-color:      rgba(0, 0, 0, 0.5);
   }
 
+
   /*-- WEBSITE HEADER + FOOTER --*/
   /* These properties only apply to Distill sites and blogs  */
 
@@ -1929,7 +1930,7 @@
     --text-color:       rgba(255, 255, 255, 0.8);
     --text-size:        15px;
     --hover-color:      white;
-    --bkgd-color:       #7D451B;
+    --bkgd-color:       #999999;
   }
 
   /*-- Additional custom styles --*/
@@ -1964,7 +1965,7 @@
   h1 {
     margin-top: 2em !important;
     font-size: 36px !important;
-    color: #7D451B !important;
+    color: #7F5539 !important;
   }
 
   d-article h1:nth-child(2) {
@@ -2242,7 +2243,7 @@ <h3>Contents</h3>
 </nav>
 </div>
 <h1 id="dependencies">Dependencies</h1>
-<p>To run our code, please install the <a href="https://www.r-project.org/">R</a> programming language and statistical computing environment (version 4.1.0). Additional required libraries are specified in each script.</p>
+<p>To run our code, please install the <a href="https://www.r-project.org/">R</a> programming language and statistical computing environment (version 4.1.0). Additional required packages are specified in each script.</p>
 <p><a href="https://www.r-project.org/" target="_blank" rel="noreferrer noopener"><img src="https://img.shields.io/badge/Language-R-276DC3?style=for-the-badge&amp;logo=r" alt="ayushnoori" align="center"/></a></p>
 <h1 id="documentation">Documentation</h1>
 <p>To read our documented code, please visit <a href="https://www.serranopozolab.org/astrocyte-review">www.serranopozolab.org/astrocyte-review</a>.</p>

diff --git a/docs/network-analysis.html b/docs/network-analysis.html
@@ -1937,6 +1937,7 @@
     --text-color:      rgba(0, 0, 0, 0.5);
   }
 
+
   /*-- WEBSITE HEADER + FOOTER --*/
   /* These properties only apply to Distill sites and blogs  */
 
@@ -1952,7 +1953,7 @@
     --text-color:       rgba(255, 255, 255, 0.8);
     --text-size:        15px;
     --hover-color:      white;
-    --bkgd-color:       #7D451B;
+    --bkgd-color:       #999999;
   }
 
   /*-- Additional custom styles --*/
@@ -1987,7 +1988,7 @@
   h1 {
     margin-top: 2em !important;
     font-size: 36px !important;
-    color: #7D451B !important;
+    color: #7F5539 !important;
   }
 
   d-article h1:nth-child(2) {
@@ -2646,7 +2647,7 @@ <h1 id="plot-circos-graph">Plot Circos Graph</h1>
 </div>
 </div>
 <h1 id="plot-chord-graph">Plot Chord Graph</h1>
-<p>First, transform network to adjacency matrix, then group by function. We also define a utility <code>merge</code> function to retrieve the group for an arbitrary set of symbols - this will be useful later.</p>
+<p>First, transform the network to an adjacency matrix, then group by function. We also define a utility <code>merge</code> function to retrieve the group for an arbitrary set of symbols - this will be useful later.</p>
 <div class="layout-chunk" data-layout="l-body">
 <div class="sourceCode">
 <pre class="sourceCode r"><code class="sourceCode r"><span class='co'># utility function to retrieve group</span>
@@ -2705,7 +2706,7 @@ <h1 id="plot-network-graph">Plot Network Graph</h1>
 </code></pre>
 </div>
 </div>
-<p>Then, create network graph.</p>
+<p>Then, create the network graph.</p>
 <div class="layout-chunk" data-layout="l-body">
 <div class="sourceCode">
 <pre class="sourceCode r"><code class="sourceCode r"><span class='co'># create network graph</span>
@@ -2736,7 +2737,7 @@ <h1 id="plot-network-graph">Plot Network Graph</h1>
 </div>
 </div>
 <h1 id="hub-gene-networks">Hub Gene Networks</h1>
-<p>Create networks for top hub markers emphasizing their connectivity. First, define a function</p>
+<p>Create networks for top hub markers which emphasize their connectivity.</p>
 <div class="layout-chunk" data-layout="l-body">
 <div class="sourceCode">
 <pre class="sourceCode r"><code class="sourceCode r"><span class='co'># remove and recreate directory if it exists</span>
@@ -2808,7 +2809,7 @@ <h1 id="hub-gene-networks">Hub Gene Networks</h1>
 </div>
 </div>
 <h1 id="interactive-network-graph">Interactive Network Graph</h1>
-<p>Create interactive network graph (with manual layout identical to above).</p>
+<p>Create an interactive network graph (with the manual layout identical to above).</p>
 <div class="layout-chunk" data-layout="l-body">
 <div class="sourceCode">
 <pre class="sourceCode r"><code class="sourceCode r"><span class='co'># get network data</span>

diff --git a/docs/omics-comparison.html b/docs/omics-comparison.html
@@ -1938,6 +1938,7 @@
     --text-color:      rgba(0, 0, 0, 0.5);
   }
 
+
   /*-- WEBSITE HEADER + FOOTER --*/
   /* These properties only apply to Distill sites and blogs  */
 
@@ -1953,7 +1954,7 @@
     --text-color:       rgba(255, 255, 255, 0.8);
     --text-size:        15px;
     --hover-color:      white;
-    --bkgd-color:       #7D451B;
+    --bkgd-color:       #999999;
   }
 
   /*-- Additional custom styles --*/
@@ -1988,7 +1989,7 @@
   h1 {
     margin-top: 2em !important;
     font-size: 36px !important;
-    color: #7D451B !important;
+    color: #7F5539 !important;
   }
 
   d-article h1:nth-child(2) {

diff --git a/docs/pathway-enrichment.html b/docs/pathway-enrichment.html
@@ -1941,6 +1941,7 @@
     --text-color:      rgba(0, 0, 0, 0.5);
   }
 
+
   /*-- WEBSITE HEADER + FOOTER --*/
   /* These properties only apply to Distill sites and blogs  */
 
@@ -1956,7 +1957,7 @@
     --text-color:       rgba(255, 255, 255, 0.8);
     --text-size:        15px;
     --hover-color:      white;
-    --bkgd-color:       #7D451B;
+    --bkgd-color:       #999999;
   }
 
   /*-- Additional custom styles --*/
@@ -1991,7 +1992,7 @@
   h1 {
     margin-top: 2em !important;
     font-size: 36px !important;
-    color: #7D451B !important;
+    color: #7F5539 !important;
   }
 
   d-article h1:nth-child(2) {
@@ -2334,16 +2335,23 @@ <h1 id="parse-pathway-enrichment-results">Parse Pathway Enrichment Results</h1>
 <div class="layout-chunk" data-layout="l-body">
 <div class="sourceCode">
 <pre class="sourceCode r"><code class="sourceCode r"><span class='co'># header style</span>
-<span class='va'>hs</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/openxlsx/man/createStyle.html'>createStyle</a></span><span class='op'>(</span>fontColour <span class='op'>=</span> <span class='st'>"#FAF3DD"</span>, fgFill <span class='op'>=</span> <span class='st'>"#337CA0"</span>, fontName <span class='op'>=</span> <span class='st'>"Arial Black"</span>, halign <span class='op'>=</span> <span class='st'>"center"</span>, valign <span class='op'>=</span> <span class='st'>"center"</span>, textDecoration <span class='op'>=</span> <span class='st'>"Bold"</span>, border <span class='op'>=</span> <span class='st'>"Bottom"</span>, borderStyle <span class='op'>=</span> <span class='st'>"thick"</span>, fontSize <span class='op'>=</span> <span class='fl'>14</span><span class='op'>)</span>
+<span class='va'>hs</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/openxlsx/man/createStyle.html'>createStyle</a></span><span class='op'>(</span>fontColour <span class='op'>=</span> <span class='st'>"#FAF3DD"</span>, fgFill <span class='op'>=</span> <span class='st'>"#337CA0"</span>,
+                 fontName <span class='op'>=</span> <span class='st'>"Arial Black"</span>, halign <span class='op'>=</span> <span class='st'>"center"</span>,
+                 valign <span class='op'>=</span> <span class='st'>"center"</span>, textDecoration <span class='op'>=</span> <span class='st'>"Bold"</span>,
+                 border <span class='op'>=</span> <span class='st'>"Bottom"</span>, borderStyle <span class='op'>=</span> <span class='st'>"thick"</span>, fontSize <span class='op'>=</span> <span class='fl'>14</span><span class='op'>)</span>
 
 <span class='co'># row style #1</span>
-<span class='va'>r1</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/openxlsx/man/createStyle.html'>createStyle</a></span><span class='op'>(</span>fontColour <span class='op'>=</span> <span class='st'>"#363635"</span>, fgFill <span class='op'>=</span> <span class='st'>"#FAF3DD"</span>, fontName <span class='op'>=</span> <span class='st'>"Arial"</span>, fontSize <span class='op'>=</span> <span class='fl'>10</span><span class='op'>)</span>
+<span class='va'>r1</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/openxlsx/man/createStyle.html'>createStyle</a></span><span class='op'>(</span>fontColour <span class='op'>=</span> <span class='st'>"#363635"</span>, fgFill <span class='op'>=</span> <span class='st'>"#FAF3DD"</span>,
+                 fontName <span class='op'>=</span> <span class='st'>"Arial"</span>, fontSize <span class='op'>=</span> <span class='fl'>10</span><span class='op'>)</span>
 
 <span class='co'># row style #2</span>
-<span class='va'>r2</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/openxlsx/man/createStyle.html'>createStyle</a></span><span class='op'>(</span>fontColour <span class='op'>=</span> <span class='st'>"#363635"</span>, fgFill <span class='op'>=</span> <span class='st'>"#C4E4E9"</span>, fontName <span class='op'>=</span> <span class='st'>"Arial"</span>, fontSize <span class='op'>=</span> <span class='fl'>10</span><span class='op'>)</span>
+<span class='va'>r2</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/openxlsx/man/createStyle.html'>createStyle</a></span><span class='op'>(</span>fontColour <span class='op'>=</span> <span class='st'>"#363635"</span>, fgFill <span class='op'>=</span> <span class='st'>"#C4E4E9"</span>,
+                 fontName <span class='op'>=</span> <span class='st'>"Arial"</span>, fontSize <span class='op'>=</span> <span class='fl'>10</span><span class='op'>)</span>
 
 <span class='co'># subheader style</span>
-<span class='va'>sh</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/openxlsx/man/createStyle.html'>createStyle</a></span><span class='op'>(</span>fontColour <span class='op'>=</span> <span class='st'>"#363635"</span>, fgFill <span class='op'>=</span> <span class='st'>"#FFA69E"</span>, fontName <span class='op'>=</span> <span class='st'>"Arial"</span>, textDecoration <span class='op'>=</span> <span class='st'>"Bold"</span>, border <span class='op'>=</span> <span class='st'>"TopBottom"</span>, borderStyle <span class='op'>=</span> <span class='st'>"thick"</span><span class='op'>)</span>
+<span class='va'>sh</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/openxlsx/man/createStyle.html'>createStyle</a></span><span class='op'>(</span>fontColour <span class='op'>=</span> <span class='st'>"#363635"</span>, fgFill <span class='op'>=</span> <span class='st'>"#FFA69E"</span>,
+                 fontName <span class='op'>=</span> <span class='st'>"Arial"</span>, textDecoration <span class='op'>=</span> <span class='st'>"Bold"</span>,
+                 border <span class='op'>=</span> <span class='st'>"TopBottom"</span>, borderStyle <span class='op'>=</span> <span class='st'>"thick"</span><span class='op'>)</span>
 </code></pre>
 </div>
 </div>
@@ -2413,7 +2421,9 @@ <h1 id="parse-pathway-enrichment-results">Parse Pathway Enrichment Results</h1>
 
   <span class='co'># rename columns for Excel workbook</span>
   <span class='va'>datWB</span> <span class='op'>=</span> <span class='fu'><a href='https://Rdatatable.gitlab.io/data.table/reference/copy.html'>copy</a></span><span class='op'>(</span><span class='va'>dat</span><span class='op'>)</span>
-  <span class='fu'><a href='https://Rdatatable.gitlab.io/data.table/reference/setattr.html'>setnames</a></span><span class='op'>(</span><span class='va'>datWB</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"ID"</span>, <span class='st'>"Pathway"</span>, <span class='st'>"K (Genes in Pathway)"</span>, <span class='st'>"k (Genes in Overlap)"</span>, <span class='st'>"k/K"</span>, <span class='st'>"p-value"</span>, <span class='st'>"FDR q-value"</span>, <span class='st'>"Cluster"</span>, <span class='st'>"Symbol"</span>, <span class='st'>"ENTREZ"</span>, <span class='st'>"Description"</span><span class='op'>)</span><span class='op'>)</span>
+  <span class='fu'><a href='https://Rdatatable.gitlab.io/data.table/reference/setattr.html'>setnames</a></span><span class='op'>(</span><span class='va'>datWB</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"ID"</span>, <span class='st'>"Pathway"</span>, <span class='st'>"K (Genes in Pathway)"</span>,
+                    <span class='st'>"k (Genes in Overlap)"</span>, <span class='st'>"k/K"</span>, <span class='st'>"p-value"</span>, <span class='st'>"FDR q-value"</span>,
+                    <span class='st'>"Cluster"</span>, <span class='st'>"Symbol"</span>, <span class='st'>"ENTREZ"</span>, <span class='st'>"Description"</span><span class='op'>)</span><span class='op'>)</span>
   <span class='va'>header</span> <span class='op'>=</span> <span class='va'>datWB</span><span class='op'>[</span>, <span class='fu'><a href='https://rdrr.io/r/base/which.html'>which</a></span><span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://Rdatatable.gitlab.io/data.table/reference/duplicated.html'>duplicated</a></span><span class='op'>(</span><span class='va'>Cluster</span><span class='op'>)</span><span class='op'>)</span><span class='op'>]</span> <span class='op'>+</span> <span class='fl'>0</span><span class='op'>:</span><span class='op'>(</span><span class='va'>nclust</span> <span class='op'>-</span> <span class='fl'>1</span><span class='op'>)</span>
 
   <span class='co'># add rows for manual annotatioN</span>
@@ -2504,7 +2514,11 @@ <h1 id="aggregate-annotated-pathways">Aggregate Annotated Pathways</h1>
 <span class='co'># refactor cluster database labels and order by -log10(FDR q-value)</span>
 <span class='va'>clusters</span> <span class='op'>=</span> <span class='va'>clusters</span> <span class='op'>%&gt;%</span>
   <span class='va'>.</span><span class='op'>[</span>, <span class='va'>ID</span> <span class='op'>:=</span> <span class='cn'>NULL</span><span class='op'>]</span> <span class='op'>%&gt;%</span>
-  <span class='va'>.</span><span class='op'>[</span>, <span class='va'>Database</span> <span class='op'>:=</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>factor</a></span><span class='op'>(</span><span class='va'>Database</span>, levels <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"GO BP"</span>, <span class='st'>"GO CC"</span>, <span class='st'>"GO MF"</span>, <span class='st'>"Reactome"</span><span class='op'>)</span>, labels <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"GO: Biological Process"</span>, <span class='st'>"GO: Cellular Component"</span>, <span class='st'>"GO: Molecular Function"</span>, <span class='st'>"Reactome"</span><span class='op'>)</span><span class='op'>)</span><span class='op'>]</span> <span class='op'>%&gt;%</span>
+  <span class='va'>.</span><span class='op'>[</span>, <span class='va'>Database</span> <span class='op'>:=</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>factor</a></span><span class='op'>(</span>
+    <span class='va'>Database</span>,
+    levels <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"GO BP"</span>, <span class='st'>"GO CC"</span>, <span class='st'>"GO MF"</span>, <span class='st'>"Reactome"</span><span class='op'>)</span>,
+    labels <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"GO: Biological Process"</span>, <span class='st'>"GO: Cellular Component"</span>,
+               <span class='st'>"GO: Molecular Function"</span>, <span class='st'>"Reactome"</span><span class='op'>)</span><span class='op'>)</span><span class='op'>]</span> <span class='op'>%&gt;%</span>
   <span class='va'>.</span><span class='op'>[</span><span class='fu'><a href='https://Rdatatable.gitlab.io/data.table/reference/setorder.html'>order</a></span><span class='op'>(</span><span class='va'>Database</span>, <span class='va'>logQ</span><span class='op'>)</span>, <span class='op'>]</span>
 </code></pre>
 </div>

diff --git a/docs/search.json b/docs/search.json
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
@@ -6,22 +6,22 @@
   </url>
   <url>
     <loc>https://serranopozolab.org/astrocyte-review/</loc>
-    <lastmod>2021-07-16T11:18:21-07:00</lastmod>
+    <lastmod>2021-07-27T15:40:32-07:00</lastmod>
   </url>
   <url>
     <loc>https://serranopozolab.org/astrocyte-review/network-analysis.html</loc>
-    <lastmod>2021-07-16T11:45:20-07:00</lastmod>
+    <lastmod>2021-07-27T15:43:20-07:00</lastmod>
   </url>
   <url>
     <loc>https://serranopozolab.org/astrocyte-review/omics-comparison.html</loc>
     <lastmod>2021-07-16T11:45:44-07:00</lastmod>
   </url>
   <url>
     <loc>https://serranopozolab.org/astrocyte-review/pathway-enrichment.html</loc>
-    <lastmod>2021-07-16T11:45:29-07:00</lastmod>
+    <lastmod>2021-07-27T15:45:53-07:00</lastmod>
   </url>
   <url>
     <loc>https://serranopozolab.org/astrocyte-review/tf-enrichment.html</loc>
-    <lastmod>2021-07-16T11:45:36-07:00</lastmod>
+    <lastmod>2021-07-27T15:52:54-07:00</lastmod>
   </url>
 </urlset>