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- <!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" />
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-
-
-
-
- class: center, middle, title
-
- # UE Visualisation
-
- ### 2019-2020
-
- ## Dr. Maxime Wack
-
- ### AHU Informatique médicale
- #### Hôpital Européen Georges Pompidou, </br> 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") -> 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) -> 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)$type <- bipartite.mapping(graphe)$type
-
- # Créer les projections
- projs <- bipartite.projection(graphe)
-
- # Séparer les projections en deux graphes
- HDN <- projs$proj1
- HGN <- projs$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 %>%
- decompose -> diseases
- ```
- ---
-
- # ggraph
-
-
- ```r
- graph_one <- function(graph)
- {
- ggraph(graph) +
- geom_edge_diagonal() +
- geom_node_label(aes(label = name))
- }
- ```
-
- ---
-
- # Filtrer sous-graphes < 10 sommets
-
-
- ```r
- diseases %>%
- keep(map_dbl(diseases, vcount) >= 10) %>%
- map(graph_one) -> plots
- ```
- ---
-
- # Malformations cardiaques
-
-
- ```r
- plots[[5]]
- ```
-
- ![](lab06_graphes_files/figure-html/cardiaques-1.png)<!-- -->
- ---
- # Surdités
-
-
- ```r
- plots[[9]]
- ```
-
- ![](lab06_graphes_files/figure-html/surdités-1.png)<!-- -->
- ---
- # Ostéogénèses imparfaites
-
-
- ```r
- plots[[12]]
- ```
-
- ![](lab06_graphes_files/figure-html/Ostéogénèses-1.png)<!-- -->
- ---
-
- # Export
-
-
- ```r
- write.graph(HDN, file = "diseases.graphml", format = "graphml")
- write.graph(HGN, file = "genes.graphml", format = "graphml")
- ```
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