Add lab 06

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courses/lab06_graphes.Rmd

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+---
+title: "Graphes"
+author: "Maxime Wack"
+date: "19/11/2019"
+output:
+  xaringan::moon_reader:
+    css: ['default','css/my_style.css']
+    lib_dir: libs
+    seal: false
+    nature:
+      ratio: '4:3'
+      countIncrementalSlides: false
+      self-contained: true
+      beforeInit: "addons/macros.js"
+      highlightLines: true
+  pdf_document:
+    seal: false
+---
+
+```{r setup, include=FALSE}
+library(tidyverse)
+library(DT)
+library(knitr)
+
+opts_chunk$set(echo = TRUE,
+               ## fig.asp= .5,
+               message = F,
+               warning = F)
+
+options(DT.options = list(paging = F,
+                          search = F,
+                          info = F))
+
+datatable <- partial(datatable, rownames = F)
+```
+
+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 libs}
+library(igraph)
+library(ggraph)
+library(tidyverse)
+```
+
+---
+class:center,middle
+# igraph
+
+---
+
+# Créer des graphes
+
+```{r create graph, eval = F}
+# 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 load}
+read_csv("lab06_data/OMIM.csv") -> OMIM
+```
+
+```{r load show, echo = F}
+OMIM %>%
+  slice(70:80) %>%
+  datatable
+```
+
+---
+# Chargement du graphe
+
+```{r graph data frame}
+graph.data.frame(OMIM, directed = F) -> graphe
+```
+
+```{r graph data frame show, echo = F}
+graphe
+```
+---
+# Informations sur le graphe
+
+### Sommets
+
+```{r vcount}
+vcount(graphe)
+```
+### Arêtes
+
+```{r ecount}
+ecount(graphe)
+```
+
+---
+# Informations sur le graphe
+
+### Dirigé ?
+
+```{r directed}
+is.directed(graphe)
+```
+
+### Voisins d'un sommet
+
+```{r neighbors}
+neighbors(graphe, V(graphe)[2019])
+```
+
+---
+# Projection
+
+```{r projection}
+# 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}
+HDN
+```
+---
+
+# HGN
+
+```{r HGN}
+HGN
+```
+---
+
+# Décomposition en sous-graphes
+
+```{r decompos}
+HDN %>%
+  decompose -> diseases
+```
+---
+
+# ggraph
+
+```{r visu}
+graph_one <- function(graph)
+{
+  ggraph(graph) +
+    geom_edge_diagonal() +
+    geom_node_label(aes(label = name))
+}
+```
+
+---
+
+# Filtrer sous-graphes < 10 sommets
+
+```{r sous-graphes par sommets}
+diseases %>%
+  keep(map_dbl(diseases, vcount) >= 10) %>%
+  map(graph_one) -> plots
+```
+---
+
+# Malformations cardiaques
+
+```{r cardiaques}
+plots[[5]]
+```
+---
+# Surdités
+
+```{r surdités}
+plots[[9]]
+```
+---
+# Ostéogénèses imparfaites
+
+```{r Ostéogénèses}
+plots[[12]]
+```
+---
+
+# Export
+
+```{r export, eval = F}
+write.graph(HDN, file = "diseases.graphml", format = "graphml")
+write.graph(HGN, file = "genes.graphml", format = "graphml")
+```