quarto week 11

3mmaRand · Dec 3, 2023 · 002cc9a · 002cc9a
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diff --git a/_site/core/week-11/example.html b/_site/core/week-11/example.html
diff --git a/_site/core/week-11/images/512px-Chaffinch_(Fringilla_coelebs).jpg b/_site/core/week-11/images/512px-Chaffinch_(Fringilla_coelebs).jpg
diff --git a/_site/core/week-11/images/512px-Fringilla_coelebs_palmae_-_Los_Tilos.jpg b/_site/core/week-11/images/512px-Fringilla_coelebs_palmae_-_Los_Tilos.jpg
diff --git a/_site/index.html b/_site/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.3.450">
+<meta name="generator" content="quarto-1.2.269">
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 <meta name="author" content="Emma Rand">
 <title>Data Analysis for Group Project - Data Analysis for the Group Research Project</title>
@@ -15,7 +15,7 @@
 ul.task-list{list-style: none;}
 ul.task-list li input[type="checkbox"] {
   width: 0.8em;
-  margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ 
+  margin: 0 0.8em 0.2em -1.6em;
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 </style>
@@ -51,8 +51,7 @@
     "search-more-matches-text": "more matches in this document",
     "search-clear-button-title": "Clear",
     "search-detached-cancel-button-title": "Cancel",
-    "search-submit-button-title": "Submit",
-    "search-label": "Search"
+    "search-submit-button-title": "Submit"
   }
 }</script><link rel="stylesheet" href="styles.css">
 </head>
@@ -65,29 +64,25 @@
     <span class="navbar-title">Data Analysis for Group Project</span>
     </a>
   </div>
-            <div id="quarto-search" class="" title="Search"></div>
           <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
   <span class="navbar-toggler-icon"></span>
 </button>
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
 <li class="nav-item">
-    <a class="nav-link active" href="./index.html" rel="" target="" aria-current="page">
+    <a class="nav-link active" href="./index.html" aria-current="page">
  <span class="menu-text">Welcome!</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="./core/core.html" rel="" target="">
+    <a class="nav-link" href="./core/core.html">
  <span class="menu-text">Core</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="./omics/omics.html" rel="" target="">
+    <a class="nav-link" href="./omics/omics.html">
  <span class="menu-text">Omics</span></a>
   </li>  
 </ul>
-<div class="quarto-navbar-tools ms-auto">
-    <a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
-    <a href="https://github.com/3mmaRand/BIO00088H-data" rel="" title="BIO00088H-data GitHub" class="quarto-navigation-tool px-1" aria-label="BIO00088H-data GitHub"><i class="bi bi-github"></i></a>
-</div>
+<div id="quarto-search" class="" title="Search"></div>
           </div> <!-- /navcollapse -->
       </div> <!-- /container-fluid -->
     </nav></header><!-- content --><div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
@@ -120,7 +115,7 @@ <h1 class="title">Data Analysis for the Group Research Project</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">30 September, 2023</p>
+      <p class="date">6 October, 2023</p>
     </div>
   </div>
 
@@ -248,23 +243,9 @@ <h1 class="title">Data Analysis for the Group Research Project</h1>
     icon: icon
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@@ -329,92 +310,6 @@ <h1 class="title">Data Analysis for the Group Research Project</h1>
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@@ -453,12 +348,12 @@ <h1 class="title">Data Analysis for the Group Research Project</h1>
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     var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
-      var filterRegex = new RegExp("^(?:http:|https:)\/\/3mmarand\.github\.io\/BIO00088H-data");
+      var filterRegex = new RegExp(/^(?:http:|https:)\/\/3mmarand\.github\.io\/BIO00088H-data/);
     var isInternal = (href) => {
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@@ -471,9 +366,6 @@ <h1 class="title">Data Analysis for the Group Research Project</h1>
 </div> <!-- /content -->
 <footer class="footer"><div class="nav-footer">
     <div class="nav-footer-left">Rand E (2023). Data Analysis for Group Project. <a href="https://3mmarand.github.io/BIO00088H-data/" class="uri">https://3mmarand.github.io/BIO00088H-data/</a>.</div>   
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diff --git a/_site/search.json b/_site/search.json
@@ -1760,5 +1760,12 @@
     "title": "Workshop",
     "section": "Visualise all the results with a volcano plot",
     "text": "Visualise all the results with a volcano plot\ncolour the points if FDR < 0.05 and prog_hspc_results > 1\n\nlibrary(ggrepel)\n\n\nprog_hspc_results <- prog_hspc_results |> \n  mutate(log10_FDR = -log10(FDR),\n         sig = FDR < 0.05,\n         bigfc = abs(summary.logFC) >= 2) \n\n\nvol <- prog_hspc_results |> \n  ggplot(aes(x = summary.logFC, \n             y = log10_FDR, \n             colour = interaction(sig, bigfc))) +\n  geom_point() +\n  geom_hline(yintercept = -log10(0.05), \n             linetype = \"dashed\") +\n  geom_vline(xintercept = 1, \n             linetype = \"dashed\") +\n  geom_vline(xintercept = -1, \n             linetype = \"dashed\") +\n  scale_x_continuous(expand = c(0, 0)) +\n  scale_y_continuous(expand = c(0, 0)) +\n  scale_colour_manual(values = c(\"gray\",\n                                 \"pink\",\n                                 \"deeppink\")) +\n  geom_text_repel(data = subset(prog_hspc_results, \n                                bigfc & sig),\n                  aes(label = external_gene_name),\n                  size = 3,\n                  max.overlaps = 50) +\n  theme_classic() +\n  theme(legend.position = \"none\")\n\n\nggsave(\"figures/prog-hspc-volcano.png\",\n       plot = vol,\n       height = 4.5, \n       width = 4.5,\n       units = \"in\",\n       device = \"png\")"
+  },
+  {
+    "objectID": "core/week-11/example.html",
+    "href": "core/week-11/example.html",
+    "title": "Example",
+    "section": "",
+    "text": "Introduction\nA number of subspecies of the common chaffinch, Fringilla coelebs, have been described based principally on the differences in the pattern and colour of the adult male plumage. Two of groups of these subspecies are:\n\n“coelebs group” that occurs in Europe and Asia\n“canariensis group” that occurs on the Canary Islands\n\n\n\n\n\n\n\n\n\n\n(a) F. c. coelebs\n\n\n\n\n\n\n\n\n\n(b) F. c. palmae\n\n\n\n\n\n\nFigure 1: Adult male Fringilla coelebs of the coelebs group on the left (Andreas Trepte, CC BY-SA 2.5 https://creativecommons.org/licenses/by-sa/2.5, via Wikimedia Commons) and of the canariensis group on the right (H. Zell, CC BY-SA 3.0 https://creativecommons.org/licenses/by-sa/3.0, via Wikimedia Commons).\n\n\nThis study aimed to determine whether there is a difference in the mass of the two subspecies.\nMethods\nWe randomly sampled 20 F. c. coelebs males and 20 F. c. palmae males and determined their mass with spring scales. Analysis was carried out with R version 4.3.1 and tidyverse (Wickham et al. 2019) packages\nResults\nCheck the assumptions: All t-tests assume the “residuals” are normally distributed and have homogeneity of variance.\nFirst use common sense: mass is a continuous and we would expect it to be normally distributed thus we would expect the residuals to be normally distributed\nSecond by plotting residuals:\nDiscussion\n\n\n\n\nReferences\n\nWickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. “Welcome to the Tidyverse” 4: 1686. https://doi.org/10.21105/joss.01686."
   }
 ]