Add generated html for course and lab 06

5 vuotta sitten · 6e4a6fc8c4
--- a/courses/06_graphes.html
+++ b/courses/06_graphes.html
@@ -0,0 +1,339 @@
 <!DOCTYPE html>
 <html xmlns="http://www.w3.org/1999/xhtml" lang="" xml:lang="">
  <head>
    <title>Graphes</title>
    <meta charset="utf-8" />
    <meta name="author" content="Maxime Wack" />
    <link href="libs/remark-css-0.0.1/default.css" rel="stylesheet" />
    <link rel="stylesheet" href="css/my_style.css" type="text/css" />
  </head>
  <body>
    <textarea id="source">




 class: center, middle, title
 # UE Visualisation
 ### 2019-2020
 ## Dr. Maxime Wack
 ### AHU Informatique médicale
 #### Hôpital Européen Georges Pompidou, &lt;/br&gt; Université de Paris

 ---
 class: center, middle
 # Objectif
 ## Théorie des graphes
 ## Créer et manipuler des graphes
 ## Représenter des graphes

 ---
 # Théorie des graphes

 ### Étude des graphes et leurs applications
 ### Topologie des graphes
 ### Propriétés des graphes
 ### Développement d'algorithmes
 - parcours en largeur/profondeur
 - calcul de trajet (A*, Dijkstra)
 - détection de sous-graphes
 - inférence, effets de réseaux
 - résolution de contraintes

 ---
 # Graphes
 .pull-left[
 ## Graphes ou réseaux
 *graphs* and *networks*
 ## Représentation de **relations** entre des **éléments**
 ]

 .pull-right[
 ![](06_img/graphe.png)
 ]

 ---
 # Sommets
 .pull-left[
 ### (ou nœuds, ou points)&lt;/br&gt; *vertex (vertices)* en anglais
 ### Servent à représenter les **éléments**
 ### Peuvent posséder des **attributs** arbitraires (label, valeurs, etc.)
 ### Des attributs peuvent être **calculés** (degré, centralité, etc.)
 ]

 .pull-right[
 ![](06_img/vertices.png)
 ]


 ---
 # Arêtes
 .pull-left[
 ### (ou liens, ou lignes)&lt;/br&gt; *edges* en anglais
 ### Servent à représenter les **relations**
 ### Peuvent également posséder des **attributs** (label, poids, etc.)
 ]

 .pull-right[
 ![](06_img/edges.png)
 ]

 ---
 # Graphe dirigé

 .pull-left[
 ### Graphe dont les arêtes ont une **direction**
 ### Arêtes **bidirectionnelles** possibles
 ]

 .pull-right[
 ![](06_img/directed.png)
 ]

 ---
 # Cycles

 .pull-left[
 ### Groupes de sommets formant un **anneau**
 ### Dans un graphe dirigé, on doit pouvoir tourner
 ]

 .pull-right[
 ![](06_img/cycle.png)
 ]


 ---
 # Clique

 .pull-left[
 ### Ensemble de sommets **tous connectés entre eux**
 ]

 .pull-right[
 ![](06_img/clique.png)
 ]

 ---
 # Graphe connecté

 .pull-left[
 ### Graphe dont **tous les sommets** forment une **clique**
 ]

 .pull-right[
 ![](06_img/connected.png)
 ]

 ---
 # Arbre

 .pull-left[
 ### Graphe ne comportant **pas de cycle**
 ### Possède une ou plusieurs **racines**
 ]

 .pull-right[
 ![](06_img/tree.png)
 ]


 ---
 # Graphe dirigé acyclique

 .pull-left[
 ### Depuis le graphe dirigé précédent
 ### Quelles arêtes supprimer pour obtenir un DAG ?
 ]

 .pull-right[
 ![](06_img/directed.png)
 ]
 ---
 # Graphe dirigé acyclique

 .pull-left[
 ### **DAG** (Directed Acyclic Graph)
 ### Structure très reconnue
 - Réseaux bayésiens
 - Arbres généalogiques
 - Systèmes de contrôle de version
 - Systèmes de workflow
 - Graphe de citations
 ]

 .pull-right[
 ![](06_img/DAG.png)
 ]

 ---
 # Représentation numérique

 .pull-left[
 ![](06_img/numbered.png)
 ]

 .pull-right[
 ## Liste de sommets

 `(1, 2, 3, 4, 5, 6, 7, 8)`

 ## Liste d'arêtes

 `((2, 1), (3, 1), (4, 1),`&lt;/br&gt;
 ` (2, 3), (4, 3), (4, 2),`&lt;/br&gt;
 ` (2, 5), (5, 2), (5, 7),`&lt;/br&gt;
 ` (6, 5), (6, 7), (7, 4),`&lt;/br&gt;
 ` (7, 8))`
 ]

 ---
 # Représentation numérique

 .pull-left[
 ![](06_img/numbered.png)
 ]

 ## Matrice d'adjacence


 ```
 ##      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
 ## [1,]    0    0    0    0    0    0    0    0
 ## [2,]    1    0    1    0    1    0    0    0
 ## [3,]    1    0    0    0    0    0    0    0
 ## [4,]    1    1    1    0    0    0    0    0
 ## [5,]    0    1    0    0    0    0    1    0
 ## [6,]    0    0    0    0    1    0    1    0
 ## [7,]    0    0    0    1    0    0    0    1
 ## [8,]    0    0    0    0    0    0    0    0
 ```
 ---
 class: center
 # Visualisation
 ## Cytoscape
 ## yEd
 ## ggraph

 ---
 # Outils externes

 ## Cytoscape

 https://cytoscape.org/

 Pour l'analyse de réseaux, orienté biologie à l'origine&lt;/br&gt;
 Visualisation de réseaux&lt;/br&gt;
 Calculs d'indicateurs&lt;/br&gt;
 Mapping d'attributs sur des propriété esthétiques

 ## yEd

 https://www.yworks.com/products/yed

 Éditeur de graphes, multiples supportés&lt;/br&gt;
 Visualisation de réseaux&lt;/br&gt;
 Nombreux algorithmes de layout&lt;/br&gt;
 Calculs d'indicateurs&lt;/br&gt;
 Mapping d'attributs sur des propriété esthétiques&lt;/br&gt;

 ---
 # ggraph

 https://ggraph.data-imaginist.com/

 ### `geom_node_*` → geom pour les sommets
 ### `geom_edge_*` → geom pour les arêtes
 ### Propriété `layout` dans `ggraph()`
    </textarea>
 <style data-target="print-only">@media screen {.remark-slide-container{display:block;}.remark-slide-scaler{box-shadow:none;}}</style>
 <script src="https://remarkjs.com/downloads/remark-latest.min.js"></script>
 <script src="addons/macros.js"></script>
 <script>var slideshow = remark.create({
 "ratio": "4:3",
 "countIncrementalSlides": false,
 "self-contained": true
 });
 if (window.HTMLWidgets) slideshow.on('afterShowSlide', function (slide) {
  window.dispatchEvent(new Event('resize'));
 });
 (function(d) {
  var s = d.createElement("style"), r = d.querySelector(".remark-slide-scaler");
  if (!r) return;
  s.type = "text/css"; s.innerHTML = "@page {size: " + r.style.width + " " + r.style.height +"; }";
  d.head.appendChild(s);
 })(document);

 (function(d) {
  var el = d.getElementsByClassName("remark-slides-area");
  if (!el) return;
  var slide, slides = slideshow.getSlides(), els = el[0].children;
  for (var i = 1; i < slides.length; i++) {
    slide = slides[i];
    if (slide.properties.continued === "true" || slide.properties.count === "false") {
      els[i - 1].className += ' has-continuation';
    }
  }
  var s = d.createElement("style");
  s.type = "text/css"; s.innerHTML = "@media print { .has-continuation { display: none; } }";
  d.head.appendChild(s);
 })(document);
 // delete the temporary CSS (for displaying all slides initially) when the user
 // starts to view slides
 (function() {
  var deleted = false;
  slideshow.on('beforeShowSlide', function(slide) {
    if (deleted) return;
    var sheets = document.styleSheets, node;
    for (var i = 0; i < sheets.length; i++) {
      node = sheets[i].ownerNode;
      if (node.dataset["target"] !== "print-only") continue;
      node.parentNode.removeChild(node);
    }
    deleted = true;
  });
 })();</script>

 <script>
 (function() {
  var links = document.getElementsByTagName('a');
  for (var i = 0; i < links.length; i++) {
    if (/^(https?:)?\/\//.test(links[i].getAttribute('href'))) {
      links[i].target = '_blank';
    }
  }
 })();
 </script>

 <script>
 slideshow._releaseMath = function(el) {
  var i, text, code, codes = el.getElementsByTagName('code');
  for (i = 0; i < codes.length;) {
    code = codes[i];
    if (code.parentNode.tagName !== 'PRE' && code.childElementCount === 0) {
      text = code.textContent;
      if (/^\\\((.|\s)+\\\)$/.test(text) || /^\\\[(.|\s)+\\\]$/.test(text) ||
          /^\$\$(.|\s)+\$\$$/.test(text) ||
          /^\\begin\{([^}]+)\}(.|\s)+\\end\{[^}]+\}$/.test(text)) {
        code.outerHTML = code.innerHTML;  // remove <code></code>
        continue;
      }
    }
    i++;
  }
 };
 slideshow._releaseMath(document);
 </script>
 <!-- dynamically load mathjax for compatibility with self-contained -->
 <script>
 (function () {
  var script = document.createElement('script');
  script.type = 'text/javascript';
  script.src  = 'https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-MML-AM_CHTML';
  if (location.protocol !== 'file:' && /^https?:/.test(script.src))
    script.src  = script.src.replace(/^https?:/, '');
  document.getElementsByTagName('head')[0].appendChild(script);
 })();
 </script>
  </body>
 </html>
--- a/courses/lab06_graphes.html
+++ b/courses/lab06_graphes.html
@@ -0,0 +1,548 @@
 <!DOCTYPE html>
 <html xmlns="http://www.w3.org/1999/xhtml" lang="" xml:lang="">
  <head>
    <title>Graphes</title>
    <meta charset="utf-8" />
    <meta name="author" content="Maxime Wack" />
    <link href="libs/remark-css-0.0.1/default.css" rel="stylesheet" />
    <script src="libs/htmlwidgets-1.5.1/htmlwidgets.js"></script>
    <script src="libs/jquery-1.12.4/jquery.min.js"></script>
    <link href="libs/datatables-css-0.0.0/datatables-crosstalk.css" rel="stylesheet" />
    <script src="libs/datatables-binding-0.10/datatables.js"></script>
    <link href="libs/dt-core-1.10.19/css/jquery.dataTables.min.css" rel="stylesheet" />
    <link href="libs/dt-core-1.10.19/css/jquery.dataTables.extra.css" rel="stylesheet" />
    <script src="libs/dt-core-1.10.19/js/jquery.dataTables.min.js"></script>
    <link href="libs/crosstalk-1.0.0/css/crosstalk.css" rel="stylesheet" />
    <script src="libs/crosstalk-1.0.0/js/crosstalk.min.js"></script>
    <link rel="stylesheet" href="css/my_style.css" type="text/css" />
  </head>
  <body>
    <textarea id="source">




 class: center, middle, title

 # UE Visualisation

 ### 2019-2020

 ## Dr. Maxime Wack

 ### AHU Informatique médicale
 #### Hôpital Européen Georges Pompidou, &lt;/br&gt; Université de Paris

 ---
 # Graphe bipartite

 .pull-left[
 ### Graphe contenant deux sets de sommets **complèment déconnectés**
 ### Dit aussi 2-coloriable
 ]

 .pull-right[
 ![](06_img/bipartite.png)
 ]

 ---
 # Projection

 .pull-left[
 ### Méthode permettant de créer **deux** graphes
 ### Les sommets d'une partie sont connectés s'ils partagent un sommet d'une autre partie
 ]

 .pull-right[
 ![](06_img/71.png)
 ]

 ---
 # Projection

 .pull-left[
 ### Méthode permettant de créer **deux** graphes
 ### Les sommets d'une partie sont connectés s'ils partagent un sommet d'une autre partie
 ]

 .pull-right[
 ![](06_img/72.png)
 ]

 ---
 # Projection

 .pull-left[
 ### Méthode permettant de créer **deux** graphes
 ### Les sommets d'une partie sont connectés s'ils partagent un sommet d'une autre partie
 ]

 .pull-right[
 ![](06_img/73.png)
 ]

 ---
 # Projection

 .pull-left[
 ### Méthode permettant de créer **deux** graphes
 ### Les sommets d'une partie sont connectés s'ils partagent un sommet d'une autre partie
 ]

 .pull-right[
 ![](06_img/74.png)
 ]

 ---
 # Projection

 .pull-left[
 ### Méthode permettant de créer **deux** graphes
 ### Les sommets d'une partie sont connectés s'ils partagent un sommet d'une autre partie
 ]

 .pull-right[
 ![](06_img/75.png)
 ]

 ---
 # Projection

 .pull-left[
 ### Méthode permettant de créer **deux** graphes
 ### Les sommets d'une partie sont connectés s'ils partagent un sommet d'une autre partie
 ]

 .pull-right[
 ![](06_img/76.png)
 ]

 ---
 # Projection

 .pull-left[
 ### Méthode permettant de créer **deux** graphes
 ### Les sommets d'une partie sont connectés s'ils partagent un sommet d'une autre partie
 ]

 .pull-right[
 ![](06_img/77.png)
 ]

 ---
 class:center
 # Projection

 .pull-right[
 ![](06_img/bipartite.png)
 ]

 ---
 class:center
 # Projection

 .pull-left[
 ![](06_img/numbered_.png)
 ]

 .pull-right[
 ![](06_img/bipartite.png)
 ]

 ---
 class:center
 # Projection

 .pull-c1[
 ![](06_img/numbered_.png)
 ]

 .pull-c2[
 ![:scale 75%](06_img/bipartite.png)
 ]

 --
 .pull-c3[
 ![:scale 65%](06_img/projection.png)
 ]

 ---

 # OMIM

 *Online Mendelian Inheritance in Men*

 Base de données d'associations connues gène ↔ phénotype

 https://omim.org

 https://maximewack.com/files/OMIM.csv

 ---
 class: center
 # The Human Disease Network

 https://www.ncbi.nlm.nih.gov/pubmed/17502601

 ![:scale 90%](06_img/HDN_principe.png)

 ---
 class: center
 # The Human Disease Network

 https://www.ncbi.nlm.nih.gov/pubmed/17502601

 ![:scale 90%](06_img/HDN.png)

 ---
 # Librairies


 ```r
 library(igraph)
 library(ggraph)
 library(tidyverse)
 ```

 ---
 class:center,middle
 # igraph

 ---

 # Créer des graphes


 ```r
 # Graphe sans arête
 graph.empty(n = 10, directed = T)

 # Graphe complètement connecté
 graph.full(n = 10, directed = F, loops = F)

 # Graphe en étoile
 graph.star(n = 10, mode = "out")
 ```

 ---
 # Chargement du graphe



 ```r
 read_csv("lab06_data/OMIM.csv") -&gt; OMIM
 ```

 <div id="htmlwidget-47d834c4dcc97d74e7ee" style="width:100%;height:auto;" class="datatables html-widget"></div>
 <script type="application/json" data-for="htmlwidget-47d834c4dcc97d74e7ee">{"x":{"filter":"none","data":[["ACYL-CoA DEHYDROGENASE, SHORT-CHAIN, DEFICIENCY OF","ADAMS-OLIVER SYNDROME 1","ADAMS-OLIVER SYNDROME 2","ADAMS-OLIVER SYNDROME 3","ADENINE PHOSPHORIBOSYLTRANSFERASE DEFICIENCY","LUNG CANCER","LUNG CANCER","LUNG CANCER","LUNG CANCER","LUNG CANCER","LUNG CANCER"],["ACADS","ARHGAP31","DOCK6","RBPJ","APRT","CYP2A6","EGFR","TNFSF6","IRF1","BRAF","ERBB2"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>Disease<\/th>\n      <th>Gene<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"paging":false,"search":false,"info":false,"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>

 ---
 # Chargement du graphe


 ```r
 graph.data.frame(OMIM, directed = F) -&gt; graphe
 ```


 ```
 ## IGRAPH 01bad3b UN-- 6288 4234 -- 
 ## + attr: name (v/c)
 ## + edges from 01bad3b (vertex names):
 ## [1] ADRENAL HYPERPLASIA, CONGENITAL, DUE TO 17-ALPHA-HYDROXYLASE DEFICIENCY--CYP17A1 
 ## [2] 17-BETA-HYDROXYSTEROID DEHYDROGENASE X DEFICIENCY                      --HSD17B10
 ## [3] 2-METHYLBUTYRYL-CoA DEHYDROGENASE DEFICIENCY                           --ACADSB  
 ## [4] THREE M SYNDROME 1                                                     --CUL7    
 ## [5] THREE M SYNDROME 2                                                     --OBSL1   
 ## [6] 3-METHYLCROTONYL-CoA CARBOXYLASE 1 DEFICIENCY                          --MCCC1   
 ## [7] 3-METHYLCROTONYL-CoA CARBOXYLASE 2 DEFICIENCY                          --MCCC2   
 ## + ... omitted several edges
 ```
 ---
 # Informations sur le graphe

 ### Sommets


 ```r
 vcount(graphe)
 ```

 ```
 ## [1] 6288
 ```
 ### Arêtes


 ```r
 ecount(graphe)
 ```

 ```
 ## [1] 4234
 ```

 ---
 # Informations sur le graphe

 ### Dirigé ?


 ```r
 is.directed(graphe)
 ```

 ```
 ## [1] FALSE
 ```

 ### Voisins d'un sommet


 ```r
 neighbors(graphe, V(graphe)[2019])
 ```

 ```
 ## + 1/6288 vertex, named, from 01bad3b:
 ## [1] SLC25A3
 ```

 ---
 # Projection


 ```r
 # Établir les types (gène, phénotype)
 V(graphe)$type &lt;- bipartite.mapping(graphe)$type

 # Créer les projections
 projs &lt;- bipartite.projection(graphe)

 # Séparer les projections en deux graphes
 HDN &lt;- projs$proj1
 HGN &lt;- projs$proj2
 ```
 ---

 # HDN


 ```r
 HDN
 ```

 ```
 ## IGRAPH 8db9c9b UNW- 3512 2839 -- 
 ## + attr: name (v/c), weight (e/n)
 ## + edges from 8db9c9b (vertex names):
 ## [1] 17-BETA-HYDROXYSTEROID DEHYDROGENASE X DEFICIENCY--MENTAL RETARDATION, X-LINKED 17           
 ## [2] 17-BETA-HYDROXYSTEROID DEHYDROGENASE X DEFICIENCY--MENTAL RETARDATION, X-LINKED, SYNDROMIC 10
 ## [3] 3-HYDROXYACYL-CoA DEHYDROGENASE DEFICIENCY       --HYPERINSULINEMIC HYPOGLYCEMIA, FAMILIAL, 4
 ## [4] 3-METHYLGLUTACONIC ACIDURIA, TYPE III            --OPTIC ATROPHY 3, AUTOSOMAL DOMINANT       
 ## [5] 46,XX SEX REVERSAL 1                             --46,XY SEX REVERSAL 1                      
 ## + ... omitted several edges
 ```
 ---

 # HGN


 ```r
 HGN
 ```

 ```
 ## IGRAPH 65dfdde UNW- 2776 2810 -- 
 ## + attr: name (v/c), weight (e/n)
 ## + edges from 65dfdde (vertex names):
 ##  [1] AKR1C2--AKR1C4   LMNA  --MYBPC3   LMNA  --ZMPSTE24 GNAS  --SSTR5   
 ##  [5] GNAS  --AIP      GNAS  --STX16    GNAS  --GNASAS1  COL2A1--COL11A2 
 ##  [9] FGFR3 --KRAS     FGFR3 --HRAS     FGFR3 --RB1      FGFR3 --PIK3CA  
 ## [13] FGFR3 --AKT1     FGFR3 --APC      FGFR3 --TP53     FGFR3 --NRAS    
 ## [17] FGFR3 --FLCN     FGFR3 --MLH3     FGFR3 --ODC1     FGFR3 --CCND1   
 ## [21] FGFR3 --PLA2G2A  FGFR3 --PTPRJ    FGFR3 --EP300    FGFR3 --BUB1B   
 ## [25] FGFR3 --TLR2     FGFR3 --TLR4     FGFR3 --AURKA    FGFR3 --BCL10   
 ## [29] FGFR3 --AXIN2    FGFR3 --PDGFRL   FGFR3 --KIT      FGFR3 --STK11   
 ## + ... omitted several edges
 ```
 ---

 # Décomposition en sous-graphes


 ```r
 HDN %&gt;%
  decompose -&gt; diseases
 ```
 ---

 # ggraph


 ```r
 graph_one &lt;- function(graph)
 {
  ggraph(graph) +
    geom_edge_diagonal() +
    geom_node_label(aes(label = name))
 }
 ```

 ---

 # Filtrer sous-graphes &lt; 10 sommets


 ```r
 diseases %&gt;%
  keep(map_dbl(diseases, vcount) &gt;= 10) %&gt;%
  map(graph_one) -&gt; plots
 ```
 ---

 # Malformations cardiaques


 ```r
 plots[[5]]
 ```

 ![](lab06_graphes_files/figure-html/cardiaques-1.png)&lt;!-- --&gt;
 ---
 # Surdités


 ```r
 plots[[9]]
 ```

 ![](lab06_graphes_files/figure-html/surdités-1.png)&lt;!-- --&gt;
 ---
 # Ostéogénèses imparfaites


 ```r
 plots[[12]]
 ```

 ![](lab06_graphes_files/figure-html/Ostéogénèses-1.png)&lt;!-- --&gt;
 ---

 # Export


 ```r
 write.graph(HDN, file = "diseases.graphml", format = "graphml")
 write.graph(HGN, file = "genes.graphml", format = "graphml")
 ```
    </textarea>
 <style data-target="print-only">@media screen {.remark-slide-container{display:block;}.remark-slide-scaler{box-shadow:none;}}</style>
 <script src="https://remarkjs.com/downloads/remark-latest.min.js"></script>
 <script src="addons/macros.js"></script>
 <script>var slideshow = remark.create({
 "ratio": "4:3",
 "countIncrementalSlides": false,
 "self-contained": true,
 "highlightLines": true
 });
 if (window.HTMLWidgets) slideshow.on('afterShowSlide', function (slide) {
  window.dispatchEvent(new Event('resize'));
 });
 (function(d) {
  var s = d.createElement("style"), r = d.querySelector(".remark-slide-scaler");
  if (!r) return;
  s.type = "text/css"; s.innerHTML = "@page {size: " + r.style.width + " " + r.style.height +"; }";
  d.head.appendChild(s);
 })(document);

 (function(d) {
  var el = d.getElementsByClassName("remark-slides-area");
  if (!el) return;
  var slide, slides = slideshow.getSlides(), els = el[0].children;
  for (var i = 1; i < slides.length; i++) {
    slide = slides[i];
    if (slide.properties.continued === "true" || slide.properties.count === "false") {
      els[i - 1].className += ' has-continuation';
    }
  }
  var s = d.createElement("style");
  s.type = "text/css"; s.innerHTML = "@media print { .has-continuation { display: none; } }";
  d.head.appendChild(s);
 })(document);
 // delete the temporary CSS (for displaying all slides initially) when the user
 // starts to view slides
 (function() {
  var deleted = false;
  slideshow.on('beforeShowSlide', function(slide) {
    if (deleted) return;
    var sheets = document.styleSheets, node;
    for (var i = 0; i < sheets.length; i++) {
      node = sheets[i].ownerNode;
      if (node.dataset["target"] !== "print-only") continue;
      node.parentNode.removeChild(node);
    }
    deleted = true;
  });
 })();
 // adds .remark-code-has-line-highlighted class to <pre> parent elements
 // of code chunks containing highlighted lines with class .remark-code-line-highlighted
 (function(d) {
  const hlines = d.querySelectorAll('.remark-code-line-highlighted');
  const preParents = [];
  const findPreParent = function(line, p = 0) {
    if (p > 1) return null; // traverse up no further than grandparent
    const el = line.parentElement;
    return el.tagName === "PRE" ? el : findPreParent(el, ++p);
  };

  for (let line of hlines) {
    let pre = findPreParent(line);
    if (pre && !preParents.includes(pre)) preParents.push(pre);
  }
  preParents.forEach(p => p.classList.add("remark-code-has-line-highlighted"));
 })(document);</script>

 <script>
 (function() {
  var links = document.getElementsByTagName('a');
  for (var i = 0; i < links.length; i++) {
    if (/^(https?:)?\/\//.test(links[i].getAttribute('href'))) {
      links[i].target = '_blank';
    }
  }
 })();
 </script>

 <script>
 slideshow._releaseMath = function(el) {
  var i, text, code, codes = el.getElementsByTagName('code');
  for (i = 0; i < codes.length;) {
    code = codes[i];
    if (code.parentNode.tagName !== 'PRE' && code.childElementCount === 0) {
      text = code.textContent;
      if (/^\\\((.|\s)+\\\)$/.test(text) || /^\\\[(.|\s)+\\\]$/.test(text) ||
          /^\$\$(.|\s)+\$\$$/.test(text) ||
          /^\\begin\{([^}]+)\}(.|\s)+\\end\{[^}]+\}$/.test(text)) {
        code.outerHTML = code.innerHTML;  // remove <code></code>
        continue;
      }
    }
    i++;
  }
 };
 slideshow._releaseMath(document);
 </script>
 <!-- dynamically load mathjax for compatibility with self-contained -->
 <script>
 (function () {
  var script = document.createElement('script');
  script.type = 'text/javascript';
  script.src  = 'https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-MML-AM_CHTML';
  if (location.protocol !== 'file:' && /^https?:/.test(script.src))
    script.src  = script.src.replace(/^https?:/, '');
  document.getElementsByTagName('head')[0].appendChild(script);
 })();
 </script>
  </body>
 </html>
--- a/courses/lab06_graphes_files/figure-html/Ostéogénèses-1.png
+++ b/courses/lab06_graphes_files/figure-html/Ostéogénèses-1.png
--- a/courses/lab06_graphes_files/figure-html/cardiaques-1.png
+++ b/courses/lab06_graphes_files/figure-html/cardiaques-1.png
--- a/courses/lab06_graphes_files/figure-html/surdités-1.png
+++ b/courses/lab06_graphes_files/figure-html/surdités-1.png
--- a/courses/libs/nouislider-7.0.10/jquery.nouislider.min.css
+++ b/courses/libs/nouislider-7.0.10/jquery.nouislider.min.css
@@ -0,0 +1,4 @@
 /*! noUiSlider - 7.0.10 - 2015-03-17 17:30:22 */


 .noUi-target,.noUi-target *{-webkit-touch-callout:none;-webkit-user-select:none;-ms-touch-action:none;-ms-user-select:none;-moz-user-select:none;-moz-box-sizing:border-box;box-sizing:border-box}.noUi-target{position:relative;direction:ltr}.noUi-base{width:100%;height:100%;position:relative}.noUi-origin{position:absolute;right:0;top:0;left:0;bottom:0}.noUi-handle{position:relative;z-index:1}.noUi-stacking .noUi-handle{z-index:10}.noUi-state-tap .noUi-origin{-webkit-transition:left .3s,top .3s;transition:left .3s,top .3s}.noUi-state-drag *{cursor:inherit!important}.noUi-base{-webkit-transform:translate3d(0,0,0);transform:translate3d(0,0,0)}.noUi-horizontal{height:10px}.noUi-horizontal .noUi-handle{width:24px;height:18px;left:-12px;top:-6px}.noUi-vertical{width:18px}.noUi-vertical .noUi-handle{width:28px;height:34px;left:-6px;top:-17px}.noUi-background{background:#FAFAFA;box-shadow:inset 0 1px 1px #f0f0f0}.noUi-connect{background:#3FB8AF;box-shadow:inset 0 0 3px rgba(51,51,51,.45);-webkit-transition:background 450ms;transition:background 450ms}.noUi-origin{border-radius:2px}.noUi-target{border-radius:4px;border:1px solid #D3D3D3;box-shadow:inset 0 1px 1px #F0F0F0,0 3px 6px -5px #BBB}.noUi-target.noUi-connect{box-shadow:inset 0 0 3px rgba(51,51,51,.45),0 3px 6px -5px #BBB}.noUi-dragable{cursor:w-resize}.noUi-vertical .noUi-dragable{cursor:n-resize}.noUi-handle{border:1px solid #D9D9D9;border-radius:3px;background:#FFF;cursor:default;box-shadow:inset 0 0 1px #FFF,inset 0 1px 7px #EBEBEB,0 3px 6px -3px #BBB}.noUi-active{box-shadow:inset 0 0 1px #FFF,inset 0 1px 7px #DDD,0 3px 6px -3px #BBB}.noUi-handle:after,.noUi-handle:before{content:"";display:block;position:absolute;height:9px;width:1px;background:#E8E7E6;left:9px;top:3.5px}.noUi-handle:after{left:12px}.noUi-vertical .noUi-handle:after,.noUi-vertical .noUi-handle:before{width:14px;height:1px;left:6px;top:14px}.noUi-vertical .noUi-handle:after{top:17px}[disabled] .noUi-connect,[disabled].noUi-connect{background:#B8B8B8}[disabled] .noUi-handle{cursor:not-allowed}
--- a/courses/libs/nouislider-7.0.10/jquery.nouislider.min.js
+++ b/courses/libs/nouislider-7.0.10/jquery.nouislider.min.js
--- a/courses/libs/selectize-0.12.0/selectize.bootstrap3.css
+++ b/courses/libs/selectize-0.12.0/selectize.bootstrap3.css
@@ -0,0 +1,401 @@
 /**
 * selectize.bootstrap3.css (v0.12.0) - Bootstrap 3 Theme
 * Copyright (c) 2013–2015 Brian Reavis & contributors
 *
 * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this
 * file except in compliance with the License. You may obtain a copy of the License at:
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software distributed under
 * the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF
 * ANY KIND, either express or implied. See the License for the specific language
 * governing permissions and limitations under the License.
 *
 * @author Brian Reavis <brian@thirdroute.com>
 */
 .selectize-control.plugin-drag_drop.multi > .selectize-input > div.ui-sortable-placeholder {
  visibility: visible !important;
  background: #f2f2f2 !important;
  background: rgba(0, 0, 0, 0.06) !important;
  border: 0 none !important;
  -webkit-box-shadow: inset 0 0 12px 4px #ffffff;
  box-shadow: inset 0 0 12px 4px #ffffff;
 }
 .selectize-control.plugin-drag_drop .ui-sortable-placeholder::after {
  content: '!';
  visibility: hidden;
 }
 .selectize-control.plugin-drag_drop .ui-sortable-helper {
  -webkit-box-shadow: 0 2px 5px rgba(0, 0, 0, 0.2);
  box-shadow: 0 2px 5px rgba(0, 0, 0, 0.2);
 }
 .selectize-dropdown-header {
  position: relative;
  padding: 3px 12px;
  border-bottom: 1px solid #d0d0d0;
  background: #f8f8f8;
  -webkit-border-radius: 4px 4px 0 0;
  -moz-border-radius: 4px 4px 0 0;
  border-radius: 4px 4px 0 0;
 }
 .selectize-dropdown-header-close {
  position: absolute;
  right: 12px;
  top: 50%;
  color: #333333;
  opacity: 0.4;
  margin-top: -12px;
  line-height: 20px;
  font-size: 20px !important;
 }
 .selectize-dropdown-header-close:hover {
  color: #000000;
 }
 .selectize-dropdown.plugin-optgroup_columns .optgroup {
  border-right: 1px solid #f2f2f2;
  border-top: 0 none;
  float: left;
  -webkit-box-sizing: border-box;
  -moz-box-sizing: border-box;
  box-sizing: border-box;
 }
 .selectize-dropdown.plugin-optgroup_columns .optgroup:last-child {
  border-right: 0 none;
 }
 .selectize-dropdown.plugin-optgroup_columns .optgroup:before {
  display: none;
 }
 .selectize-dropdown.plugin-optgroup_columns .optgroup-header {
  border-top: 0 none;
 }
 .selectize-control.plugin-remove_button [data-value] {
  position: relative;
  padding-right: 24px !important;
 }
 .selectize-control.plugin-remove_button [data-value] .remove {
  z-index: 1;
  /* fixes ie bug (see #392) */
  position: absolute;
  top: 0;
  right: 0;
  bottom: 0;
  width: 17px;
  text-align: center;
  font-weight: bold;
  font-size: 12px;
  color: inherit;
  text-decoration: none;
  vertical-align: middle;
  display: inline-block;
  padding: 1px 0 0 0;
  border-left: 1px solid rgba(0, 0, 0, 0);
  -webkit-border-radius: 0 2px 2px 0;
  -moz-border-radius: 0 2px 2px 0;
  border-radius: 0 2px 2px 0;
  -webkit-box-sizing: border-box;
  -moz-box-sizing: border-box;
  box-sizing: border-box;
 }
 .selectize-control.plugin-remove_button [data-value] .remove:hover {
  background: rgba(0, 0, 0, 0.05);
 }
 .selectize-control.plugin-remove_button [data-value].active .remove {
  border-left-color: rgba(0, 0, 0, 0);
 }
 .selectize-control.plugin-remove_button .disabled [data-value] .remove:hover {
  background: none;
 }
 .selectize-control.plugin-remove_button .disabled [data-value] .remove {
  border-left-color: rgba(77, 77, 77, 0);
 }
 .selectize-control {
  position: relative;
 }
 .selectize-dropdown,
 .selectize-input,
 .selectize-input input {
  color: #333333;
  font-family: inherit;
  font-size: inherit;
  line-height: 20px;
  -webkit-font-smoothing: inherit;
 }
 .selectize-input,
 .selectize-control.single .selectize-input.input-active {
  background: #ffffff;
  cursor: text;
  display: inline-block;
 }
 .selectize-input {
  border: 1px solid #cccccc;
  padding: 6px 12px;
  display: inline-block;
  width: 100%;
  overflow: hidden;
  position: relative;
  z-index: 1;
  -webkit-box-sizing: border-box;
  -moz-box-sizing: border-box;
  box-sizing: border-box;
  -webkit-box-shadow: none;
  box-shadow: none;
  -webkit-border-radius: 4px;
  -moz-border-radius: 4px;
  border-radius: 4px;
 }
 .selectize-control.multi .selectize-input.has-items {
  padding: 5px 12px 2px;
 }
 .selectize-input.full {
  background-color: #ffffff;
 }
 .selectize-input.disabled,
 .selectize-input.disabled * {
  cursor: default !important;
 }
 .selectize-input.focus {
  -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.15);
  box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.15);
 }
 .selectize-input.dropdown-active {
  -webkit-border-radius: 4px 4px 0 0;
  -moz-border-radius: 4px 4px 0 0;
  border-radius: 4px 4px 0 0;
 }
 .selectize-input > * {
  vertical-align: baseline;
  display: -moz-inline-stack;
  display: inline-block;
  zoom: 1;
  *display: inline;
 }
 .selectize-control.multi .selectize-input > div {
  cursor: pointer;
  margin: 0 3px 3px 0;
  padding: 1px 3px;
  background: #efefef;
  color: #333333;
  border: 0 solid rgba(0, 0, 0, 0);
 }
 .selectize-control.multi .selectize-input > div.active {
  background: #428bca;
  color: #ffffff;
  border: 0 solid rgba(0, 0, 0, 0);
 }
 .selectize-control.multi .selectize-input.disabled > div,
 .selectize-control.multi .selectize-input.disabled > div.active {
  color: #808080;
  background: #ffffff;
  border: 0 solid rgba(77, 77, 77, 0);
 }
 .selectize-input > input {
  display: inline-block !important;
  padding: 0 !important;
  min-height: 0 !important;
  max-height: none !important;
  max-width: 100% !important;
  margin: 0 !important;
  text-indent: 0 !important;
  border: 0 none !important;
  background: none !important;
  line-height: inherit !important;
  -webkit-user-select: auto !important;
  -webkit-box-shadow: none !important;
  box-shadow: none !important;
 }
 .selectize-input > input::-ms-clear {
  display: none;
 }
 .selectize-input > input:focus {
  outline: none !important;
 }
 .selectize-input::after {
  content: ' ';
  display: block;
  clear: left;
 }
 .selectize-input.dropdown-active::before {
  content: ' ';
  display: block;
  position: absolute;
  background: #ffffff;
  height: 1px;
  bottom: 0;
  left: 0;
  right: 0;
 }
 .selectize-dropdown {
  position: absolute;
  z-index: 10;
  border: 1px solid #d0d0d0;
  background: #ffffff;
  margin: -1px 0 0 0;
  border-top: 0 none;
  -webkit-box-sizing: border-box;
  -moz-box-sizing: border-box;
  box-sizing: border-box;
  -webkit-box-shadow: 0 1px 3px rgba(0, 0, 0, 0.1);
  box-shadow: 0 1px 3px rgba(0, 0, 0, 0.1);
  -webkit-border-radius: 0 0 4px 4px;
  -moz-border-radius: 0 0 4px 4px;
  border-radius: 0 0 4px 4px;
 }
 .selectize-dropdown [data-selectable] {
  cursor: pointer;
  overflow: hidden;
 }
 .selectize-dropdown [data-selectable] .highlight {
  background: rgba(255, 237, 40, 0.4);
  -webkit-border-radius: 1px;
  -moz-border-radius: 1px;
  border-radius: 1px;
 }
 .selectize-dropdown [data-selectable],
 .selectize-dropdown .optgroup-header {
  padding: 3px 12px;
 }
 .selectize-dropdown .optgroup:first-child .optgroup-header {
  border-top: 0 none;
 }
 .selectize-dropdown .optgroup-header {
  color: #777777;
  background: #ffffff;
  cursor: default;
 }
 .selectize-dropdown .active {
  background-color: #f5f5f5;
  color: #262626;
 }
 .selectize-dropdown .active.create {
  color: #262626;
 }
 .selectize-dropdown .create {
  color: rgba(51, 51, 51, 0.5);
 }
 .selectize-dropdown-content {
  overflow-y: auto;
  overflow-x: hidden;
  max-height: 200px;
 }
 .selectize-control.single .selectize-input,
 .selectize-control.single .selectize-input input {
  cursor: pointer;
 }
 .selectize-control.single .selectize-input.input-active,
 .selectize-control.single .selectize-input.input-active input {
  cursor: text;
 }
 .selectize-control.single .selectize-input:after {
  content: ' ';
  display: block;
  position: absolute;
  top: 50%;
  right: 17px;
  margin-top: -3px;
  width: 0;
  height: 0;
  border-style: solid;
  border-width: 5px 5px 0 5px;
  border-color: #333333 transparent transparent transparent;
 }
 .selectize-control.single .selectize-input.dropdown-active:after {
  margin-top: -4px;
  border-width: 0 5px 5px 5px;
  border-color: transparent transparent #333333 transparent;
 }
 .selectize-control.rtl.single .selectize-input:after {
  left: 17px;
  right: auto;
 }
 .selectize-control.rtl .selectize-input > input {
  margin: 0 4px 0 -2px !important;
 }
 .selectize-control .selectize-input.disabled {
  opacity: 0.5;
  background-color: #ffffff;
 }
 .selectize-dropdown,
 .selectize-dropdown.form-control {
  height: auto;
  padding: 0;
  margin: 2px 0 0 0;
  z-index: 1000;
  background: #ffffff;
  border: 1px solid #cccccc;
  border: 1px solid rgba(0, 0, 0, 0.15);
  -webkit-border-radius: 4px;
  -moz-border-radius: 4px;
  border-radius: 4px;
  -webkit-box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175);
  box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175);
 }
 .selectize-dropdown .optgroup-header {
  font-size: 12px;
  line-height: 1.42857143;
 }
 .selectize-dropdown .optgroup:first-child:before {
  display: none;
 }
 .selectize-dropdown .optgroup:before {
  content: ' ';
  display: block;
  height: 1px;
  margin: 9px 0;
  overflow: hidden;
  background-color: #e5e5e5;
  margin-left: -12px;
  margin-right: -12px;
 }
 .selectize-dropdown-content {
  padding: 5px 0;
 }
 .selectize-dropdown-header {
  padding: 6px 12px;
 }
 .selectize-input {
  min-height: 34px;
 }
 .selectize-input.dropdown-active {
  -webkit-border-radius: 4px;
  -moz-border-radius: 4px;
  border-radius: 4px;
 }
 .selectize-input.dropdown-active::before {
  display: none;
 }
 .selectize-input.focus {
  border-color: #66afe9;
  outline: 0;
  -webkit-box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);
  box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);
 }
 .has-error .selectize-input {
  border-color: #a94442;
  -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
  box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
 }
 .has-error .selectize-input:focus {
  border-color: #843534;
  -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #ce8483;
  box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #ce8483;
 }
 .selectize-control.multi .selectize-input.has-items {
  padding-left: 9px;
  padding-right: 9px;
 }
 .selectize-control.multi .selectize-input > div {
  -webkit-border-radius: 3px;
  -moz-border-radius: 3px;
  border-radius: 3px;
 }
 .form-control.selectize-control {
  padding: 0;
  height: auto;
  border: none;
  background: none;
  -webkit-box-shadow: none;
  box-shadow: none;
  -webkit-border-radius: 0;
  -moz-border-radius: 0;
  border-radius: 0;
 }
--- a/courses/libs/selectize-0.12.0/selectize.min.js
+++ b/courses/libs/selectize-0.12.0/selectize.min.js