HEGP
/
dataviz


			
							<!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>