Merge branch 'master' of https://github.com/RockefellerUniversity/Int…

…ro_To_R_1Day
RockefellerUniversity · Feb 1, 2024 · 7bac86c · 7bac86c
2 parents be24024 + 31d6570
commit 7bac86c
Show file tree

Hide file tree

Showing 14 changed files with 234 additions and 160 deletions.
diff --git a/docs/data/writeThisMultipleXLSX.xlsx b/docs/data/writeThisMultipleXLSX.xlsx
diff --git a/docs/data/writeThisXLSX.xlsx b/docs/data/writeThisXLSX.xlsx
diff --git a/docs/presentations/r_code/introToR_Session2.R b/docs/presentations/r_code/introToR_Session2.R
@@ -6,6 +6,16 @@ suppressPackageStartupMessages(require(knitr))
 knitr::opts_chunk$set(echo = TRUE, tidy = T)
 
 
+## ----xaringan-themer, include=FALSE, warning=FALSE----------------------------
+library(xaringanthemer)
+style_mono_accent(
+  base_color = "#23373B",
+  header_font_google = google_font("Montserrat"),
+  text_font_google   = google_font("Fira Sans", "300", "300i"),
+  code_font_google   = google_font("Fira Code")
+)
+
+
 ## ----results='asis',include=TRUE,echo=FALSE-----------------------------------
 if(params$isSlides != "yes"){
   cat("# Introduction to R (part 2)

diff --git a/docs/presentations/singlepage/introToR_Session1.html b/docs/presentations/singlepage/introToR_Session1.html
@@ -9,7 +9,10 @@
 <meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
 
 
-<meta name="author" content="Rockefeller University, Bioinformatics Resource Center" />
+<meta name="author" content="Rockefeller University" />
+<meta name="author" content="Bioinformatics Resource Center" />
+<meta name="author" content="http://rockefelleruniversity.github.io/Intro_To_R_1Day/" />
+<meta name="author" content="brc@rockefeller.edu" />
 
 
 <title>Introduction to R, Session 1</title>
@@ -1556,9 +1559,10 @@
 
 
 <h1 class="title toc-ignore">Introduction to R, Session 1</h1>
-<h4 class="author">Rockefeller University, Bioinformatics Resource
-Center</h4>
-<h4 class="date"><a href="http://rockefelleruniversity.github.io/Intro_To_R_1Day/" class="uri">http://rockefelleruniversity.github.io/Intro_To_R_1Day/</a></h4>
+<h4 class="author">Rockefeller University</h4>
+<h4 class="author">Bioinformatics Resource Center</h4>
+<h4 class="author"><a href="http://rockefelleruniversity.github.io/Intro_To_R_1Day/" class="uri">http://rockefelleruniversity.github.io/Intro_To_R_1Day/</a></h4>
+<h4 class="author"><a href="mailto:brc@rockefeller.edu" class="email">brc@rockefeller.edu</a></h4>
 
 </div>
 
@@ -3004,111 +3008,111 @@ <h2>Data from external sources</h2>
 Gene_a
 </td>
 <td style="text-align:right;">
-3.131664
+3.439713
 </td>
 <td style="text-align:right;">
-4.037782
+3.282817
 </td>
 <td style="text-align:right;">
-4.794836
+2.029076
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_b
 </td>
 <td style="text-align:right;">
-4.485000
+5.183143
 </td>
 <td style="text-align:right;">
-1.574353
+4.045740
 </td>
 <td style="text-align:right;">
-3.796876
+3.695944
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_c
 </td>
 <td style="text-align:right;">
-4.247558
+2.869225
 </td>
 <td style="text-align:right;">
-2.222445
+4.664638
 </td>
 <td style="text-align:right;">
-6.111919
+2.539172
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_d
 </td>
 <td style="text-align:right;">
-2.981276
+4.693789
 </td>
 <td style="text-align:right;">
-4.555480
+4.356273
 </td>
 <td style="text-align:right;">
-4.123341
+5.969694
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_e
 </td>
 <td style="text-align:right;">
-9.667122
+10.277959
 </td>
 <td style="text-align:right;">
-11.034829
+9.973955
 </td>
 <td style="text-align:right;">
-10.846463
+11.179049
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_f
 </td>
 <td style="text-align:right;">
-11.046485
+9.782953
 </td>
 <td style="text-align:right;">
-10.704920
+10.862418
 </td>
 <td style="text-align:right;">
-10.113150
+10.499444
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_g
 </td>
 <td style="text-align:right;">
-8.596922
+10.777056
 </td>
 <td style="text-align:right;">
-10.337665
+8.521394
 </td>
 <td style="text-align:right;">
-11.694577
+10.486373
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_h
 </td>
 <td style="text-align:right;">
-9.918383
+11.717774
 </td>
 <td style="text-align:right;">
-11.110133
+10.323903
 </td>
 <td style="text-align:right;">
-11.051736
+11.212961
 </td>
 </tr>
 </tbody>

diff --git a/docs/presentations/singlepage/introToR_Session2.html b/docs/presentations/singlepage/introToR_Session2.html
@@ -9,10 +9,13 @@
 <meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
 
 
-<meta name="author" content="Rockefeller University, Bioinformatics Resource Centre" />
+<meta name="author" content="Rockefeller University" />
+<meta name="author" content="Bioinformatics Resource Center" />
+<meta name="author" content="http://rockefelleruniversity.github.io/Intro_To_R_1Day/" />
+<meta name="author" content="brc@rockefeller.edu" />
 
 
-<title>Introduction to R, Session 2 ¶  ¶ ¶  ¶ </title>
+<title>Introduction to R, Session 2</title>
 
 <script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
 // be compatible with the behavior of Pandoc < 2.8).
@@ -1555,11 +1558,11 @@
 
 
 
-<h1 class="title toc-ignore">Introduction to R, Session 2 ¶ <html> ¶ ¶
-<hr color="#EB811B" size="1px" width="796px"> ¶ </html></h1>
-<h4 class="author">Rockefeller University, Bioinformatics Resource
-Centre</h4>
-<h4 class="date"><a href="http://rockefelleruniversity.github.io/Intro_To_R_1Day/" class="uri">http://rockefelleruniversity.github.io/Intro_To_R_1Day/</a></h4>
+<h1 class="title toc-ignore">Introduction to R, Session 2</h1>
+<h4 class="author">Rockefeller University</h4>
+<h4 class="author">Bioinformatics Resource Center</h4>
+<h4 class="author"><a href="http://rockefelleruniversity.github.io/Intro_To_R_1Day/" class="uri">http://rockefelleruniversity.github.io/Intro_To_R_1Day/</a></h4>
+<h4 class="author"><a href="mailto:brc@rockefeller.edu" class="email">brc@rockefeller.edu</a></h4>
 
 </div>
 
@@ -2389,8 +2392,8 @@ <h2>Custom function example</h2>
 <span id="cb156-10"><a href="#cb156-10" aria-hidden="true" tabindex="-1"></a>A <span class="ot">&lt;-</span> <span class="fu">rnorm</span>(<span class="dv">20</span>)</span>
 <span id="cb156-11"><a href="#cb156-11" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb156-12"><a href="#cb156-12" aria-hidden="true" tabindex="-1"></a><span class="fu">my_zscore</span>(<span class="at">my_number=</span>A[<span class="dv">1</span>], <span class="at">my_vector=</span>A)</span></code></pre></div>
-<pre><code>## Mean is 0.234377094749696</code></pre>
-<pre><code>## [1] -0.9715912</code></pre>
+<pre><code>## Mean is 0.267745483307702</code></pre>
+<pre><code>## [1] -1.659081</code></pre>
 </div>
 <div id="debugging-functions" class="section level2">
 <h2>Debugging functions</h2>
@@ -2405,10 +2408,10 @@ <h2>Debugging functions</h2>
 <h2>Custom functions and apply</h2>
 <p>These custom functions can also be utilized with apply.</p>
 <div class="sourceCode" id="cb160"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb160-1"><a href="#cb160-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sapply</span>(A, my_zscore, <span class="at">my_vector=</span>A)</span></code></pre></div>
-<pre><code>##  [1] -0.97159116  0.32385300  0.09273780 -1.43723828  0.77615773  0.23989367
-##  [7] -0.28025630 -0.27637826 -0.85384484 -0.78851036  0.64910588 -0.41752804
-## [13]  0.06011209 -0.10467610 -0.04418539 -1.87700202  2.55462255  0.04428067
-## [19]  1.59037277  0.72007461</code></pre>
+<pre><code>##  [1] -1.659081312 -0.521385758  0.774612930  2.861772431  0.131227763
+##  [6]  0.495242611  0.474716884 -1.327482755  0.251037466 -0.085124417
+## [11]  0.001984395 -0.571234827  0.213895134 -0.078139969  0.143146443
+## [16] -0.550726452 -0.859529265  0.229768762  1.335560013 -1.260260075</code></pre>
 </div>
 </div>
 <div id="getting-additional-libraries" class="section level1">

diff --git a/docs/presentations/slides/introToR_Session1.html b/docs/presentations/slides/introToR_Session1.html
@@ -3,7 +3,10 @@
   <head>
     <title>Introduction to R, Session 1</title>
     <meta charset="utf-8" />
-    <meta name="author" content="Rockefeller University, Bioinformatics Resource Center" />
+    <meta name="author" content="Rockefeller University" />
+    <meta name="author" content="Bioinformatics Resource Center" />
+    <meta name="author" content="http://rockefelleruniversity.github.io/Intro_To_R_1Day/" />
+    <meta name="author" content="brc@rockefeller.edu" />
     <script src="introToR_Session1_files/header-attrs-2.25/header-attrs.js"></script>
     <link rel="stylesheet" href="xaringan-themer.css" type="text/css" />
   </head>
@@ -15,11 +18,17 @@
 # Introduction to R, Session 1
 ]
 .author[
-### Rockefeller University, Bioinformatics Resource Center
+### Rockefeller University
 ]
-.date[
+.author[
+### Bioinformatics Resource Center
+]
+.author[
 ### <a href="http://rockefelleruniversity.github.io/Intro_To_R_1Day/" class="uri">http://rockefelleruniversity.github.io/Intro_To_R_1Day/</a>
 ]
+.author[
+### <a href="mailto:brc@rockefeller.edu" class="email">brc@rockefeller.edu</a>
+]
 
 ---
 
@@ -2557,51 +2566,51 @@
 &lt;tbody&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_a &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 3.071682 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 4.659947 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 6.657631 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 4.261637 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 3.300825 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 3.946601 &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_b &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 4.386384 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 2.508203 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 4.048541 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 4.410959 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 3.596112 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 5.517069 &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_c &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 2.613734 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 3.306210 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 2.390803 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 4.629722 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 4.858954 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 3.826554 &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_d &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 6.128499 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 4.726705 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 4.703866 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 3.994964 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 4.337427 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 3.488050 &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_e &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 13.447738 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 9.166767 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 8.836641 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 9.761664 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 11.711170 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 10.553195 &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_f &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 9.654917 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 8.884562 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 11.638120 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 9.778864 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 9.115707 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 8.200663 &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_g &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 9.041328 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 8.981967 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 8.196116 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 10.734559 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 7.963840 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 9.347527 &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_h &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 9.838471 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 8.516912 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 9.739770 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 12.230264 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 10.249766 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 10.202094 &lt;/td&gt;
   &lt;/tr&gt;
 &lt;/tbody&gt;
 &lt;/table&gt;