HEGP
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dataviz

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class: center, middle, title

# UE Visualisation

### 2020-2021

## 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-4e9bb6da534171530ca8" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-4e9bb6da534171530ca8">{"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 1a34d81 UN-- 6288 4234 -- 
## + attr: name (v/c)
## + edges from 1a34d81 (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 1a34d81:
## [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 de908b5 UNW- 3512 2839 -- 
## + attr: name (v/c), weight (e/n)
## + edges from de908b5 (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 54560af UNW- 2776 2810 -- 
## + attr: name (v/c), weight (e/n)
## + edges from 54560af (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")
```
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