Started working on overview chapter

Plant-Food-Research-Open · Mar 8, 2024 · f2cd518 · f2cd518
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diff --git a/_quarto.yml b/_quarto.yml
@@ -10,6 +10,7 @@ book:
   sharing: [twitter]
   chapters:
     - index.qmd
+    - overview.qmd
     - example_dataset.qmd
     - part: "Data preparation"
       chapters:

diff --git a/_targets.R b/_targets.R
@@ -763,5 +763,18 @@ list(
       "MOFA (supervised pref.)" = mofa_output,
       "MOFA (unsupervised pref.)" = mofa_unsupervised_output
     )
+  ),
+
+  ##====================##
+  ## For walkthrough    ----
+  ##====================##
+
+  tar_target(
+    interesting_features,
+    get_top_features(
+      diablo_output,
+      n_features = 5,
+      latent_dimensions = "Component 1") |>
+      dplyr::pull(feature_id)
   )
 )
diff --git a/_targets/meta/meta b/_targets/meta/meta
@@ -47,6 +47,7 @@ individual_splsda_perf_746586a5|branch|ca46d907d7ee14e8|f44bca7322f5e277|da53f8a
 individual_splsda_run|pattern|19d2e5a4975b88a4|daafd73eccc1a544||-1224126645||||39582018|rds|local|list||individual_splsda_run_fe6f99fe*individual_splsda_run_4a7ecf19|0.695||
 individual_splsda_run_4a7ecf19|branch|7e0a4e3d819dd4ca|daafd73eccc1a544|abdf9eca33556041|-1795274176||t19740.1338336227s|fd667fed47369bab|4784480|rds|local|list|individual_splsda_run||0.23||
 individual_splsda_run_fe6f99fe|branch|d9a25069c6365467|daafd73eccc1a544|ef3d7bbeafbb777e|-1795258471||t19775.0793707498s|3519cd7663129cca|39582018|rds|local|list|individual_splsda_run||0.695||
+interesting_features|stem|2873dd1bf9256aad|a9a5d5762f34e4b1|93364749491ec80e|-1974613992||t19790.1243604917s|4a62745a16bcf9e1|179|rds|local|vector|||0.071||
 mad_mat|pattern|1e61f5902421909b|c1c091fc70d5003a||696742516||||12225506|rds|local|list||mad_mat_e428ef62*mad_mat_d5a0e3cc|0.022||
 mad_mat_d5a0e3cc|branch|d409110391e22abd|c1c091fc70d5003a|3965053855035448|663985671||t19775.0931120027s|3a25ff56c2ab5341|1708251|rds|local|list|mad_mat||0.014||
 mad_mat_e428ef62|branch|c9bd47eae2deeffa|c1c091fc70d5003a|dad11668fde6c644|588923247||t19775.0931035751s|bf4c9e55261122d9|10517255|rds|local|list|mad_mat||0.008||

diff --git a/docs/images/input_data_example.png b/docs/images/input_data_example.png
diff --git a/docs/index.html b/docs/index.html
@@ -90,7 +90,7 @@
 <script src="site_libs/quarto-search/fuse.min.js"></script>
 <script src="site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="./">
-<link href="./example_dataset.html" rel="next">
+<link href="./walkthrough.html" rel="next">
 <script src="site_libs/quarto-html/quarto.js"></script>
 <script src="site_libs/quarto-html/popper.min.js"></script>
 <script src="site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -153,7 +153,12 @@ <h1 class="quarto-secondary-nav-title">The <code>moiraine</code> R package user
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./example_dataset.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">The example dataset</span></a>
+  <a href="./walkthrough.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Integration with DIABLO</span></a>
+  </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./example_dataset.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">The example dataset</span></a>
   </div>
 </li>
         <li class="sidebar-item sidebar-item-section">
@@ -166,27 +171,27 @@ <h1 class="quarto-secondary-nav-title">The <code>moiraine</code> R package user
       <ul id="quarto-sidebar-section-1" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./data_import.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Importing data</span></a>
+  <a href="./data_import.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Importing data</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./inspecting_multidataset.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Inspecting the <code>MultiDataSet</code> object</span></a>
+  <a href="./inspecting_multidataset.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Inspecting the <code>MultiDataSet</code> object</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./modifying_multidataset.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Modifying the <code>MultiDataSet</code> object</span></a>
+  <a href="./modifying_multidataset.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Modifying the <code>MultiDataSet</code> object</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./preprocessing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Data pre-processing</span></a>
+  <a href="./preprocessing.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Data pre-processing</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./prefiltering.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Dataset pre-filtering</span></a>
+  <a href="./prefiltering.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Dataset pre-filtering</span></a>
   </div>
 </li>
       </ul>
@@ -201,17 +206,17 @@ <h1 class="quarto-secondary-nav-title">The <code>moiraine</code> R package user
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./spls.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Integration with sPLS</span></a>
+  <a href="./spls.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Integration with sPLS</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./so2pls.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Integration with sO2PLS</span></a>
+  <a href="./so2pls.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Integration with sO2PLS</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./mofa.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Integration with MOFA</span></a>
+  <a href="./mofa.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Integration with MOFA</span></a>
   </div>
 </li>
       </ul>
@@ -226,7 +231,7 @@ <h1 class="quarto-secondary-nav-title">The <code>moiraine</code> R package user
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./diablo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Integration with DIABLO</span></a>
+  <a href="./diablo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Integration with DIABLO</span></a>
   </div>
 </li>
       </ul>
@@ -241,17 +246,17 @@ <h1 class="quarto-secondary-nav-title">The <code>moiraine</code> R package user
       <ul id="quarto-sidebar-section-4" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./interpretation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Interpreting the integration results</span></a>
+  <a href="./interpretation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">12</span>&nbsp; <span class="chapter-title">Interpreting the integration results</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./evaluation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">12</span>&nbsp; <span class="chapter-title">Evaluating the integration results</span></a>
+  <a href="./evaluation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">13</span>&nbsp; <span class="chapter-title">Evaluating the integration results</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./comparison.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">13</span>&nbsp; <span class="chapter-title">Comparing the integration results</span></a>
+  <a href="./comparison.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">14</span>&nbsp; <span class="chapter-title">Comparing the integration results</span></a>
   </div>
 </li>
       </ul>
@@ -499,8 +504,8 @@ <h1 class="title d-none d-lg-block">The <code>moiraine</code> R package user man
 </script><nav class="page-navigation"><div class="nav-page nav-page-previous">
   </div>
   <div class="nav-page nav-page-next">
-      <a href="./example_dataset.html" class="pagination-link">
-        <span class="nav-page-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">The example dataset</span></span> <i class="bi bi-arrow-right-short"></i>
+      <a href="./walkthrough.html" class="pagination-link">
+        <span class="nav-page-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Integration with DIABLO</span></span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>