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ptite cerise sur le gateaux

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thaaoblues 2025-01-17 11:22:12 +01:00
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Projet.Rmd
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@ -725,29 +725,32 @@ DataExpMoy$GeneID = rownames(DataExpMoy)
# stoquage plus utile du clustering
DataExpMoy$Cluster = as.factor(res_kmeans_2$cluster)
# Transforme les données de format large en format long. Chaque colonne (sauf Cluster et GeneID) devient une ligne.
data_long = pivot_longer(
# on transforme les données de format large en format long,
# on renomme la colonne des variables => pratique pour ce qu'on fait après (mais pas indispensable car elle s'appelle "variable" par défaut)
data_long = melt(
DataExpMoy,
cols = -c(Cluster, GeneID),
names_to = "Condition",
values_to = "Expression"
variable.name = "Relevé",
value.name = "Expression"
)
# Sépare la colonne "Condition" en deux nouvelles colonnes : "Traitement" et "Temps", en utilisant "_" comme séparateur.
# on sépare la colonne "Relevé" en deux nouvelles colonnes "Traitement" et "Temps", en utilisant "_" comme séparateur pour pouvoir faire un graphe en fonction du temps
# et 1 par traitement
data_long = separate(
data_long,
col = "Condition",
col = "Relevé",
into = c("Traitement", "Temps"),
sep = "_"
)
# Convertit les valeurs de la colonne Temps en nombres après avoir supprimé le suffixe "H".
# convertit les valeurs de la colonne Temps en nombres après avoir supprimé le "H" du numéro des heures
# pour cela, on ustilise gsub qui permet de match des expressions regulières
data_long$Temps = as.numeric(gsub("H", "", data_long$Temps))
# Groupe les données par Cluster, Traitement et Temps
# groupe les données par Cluster, Traitement et Temps
data_grouped = group_by(data_long, Cluster, Traitement, Temps)
# Calcule la moyenne de l'expression génique pour chaque combinaison de Cluster, Traitement et Temps. Chaque moyenne va donner un point du graphe.
# calcule la moyenne de l'expression génique pour chaque combinaison de Cluster, Traitement et Temps. Chaque moyenne va donner un point du graphe
data_mean = summarise(
data_grouped,
Expression = mean(Expression),
@ -814,39 +817,33 @@ set.seed(1234)
DataExpMoy$Cluster = as.factor(res_kmeans_3$cluster)
# Transforme les données de format large en format long. Chaque colonne (sauf Cluster et GeneID) devient une ligne.
data_long = pivot_longer(
data_long = melt(
DataExpMoy,
cols = -c(Cluster, GeneID),
names_to = "Condition",
values_to = "Expression"
variable.name = "Relevé",
value.name = "Expression"
)
# Sépare la colonne "Condition" en deux nouvelles colonnes : "Traitement" et "Temps", en utilisant "_" comme séparateur.
data_long = separate(
data_long,
col = "Condition",
col = "Relevé",
into = c("Traitement", "Temps"),
sep = "_"
)
# Convertit les valeurs de la colonne Temps en nombres après avoir supprimé le suffixe "H".
data_long$Temps = as.numeric(gsub("H", "", data_long$Temps))
# Groupe les données par Cluster, Traitement et Temps
data_grouped = group_by(data_long, Cluster, Traitement, Temps)
# Calcule la moyenne de l'expression génique pour chaque combinaison de Cluster, Traitement et Temps. Chaque moyenne va donner un point du graphe.
data_mean = summarise(
data_grouped,
Expression = mean(Expression),
.groups = "drop"
)
# plot
ggplot(data_mean, aes(x = Temps, y = Expression, group = Cluster, color = Cluster)) +
geom_line(size = 1.2) +
facet_wrap(~ Traitement, scales = "free_y") + # va créer un sous graphique pour chaque traitement, sans forcément la même échelle sur l'axe y
facet_wrap(~ Traitement, scales = "free_y") +
labs(
x = "Temps (heures)",
y = "Expression génique (moyenne)"
@ -860,10 +857,14 @@ ggplot(data_mean, aes(x = Temps, y = Expression, group = Cluster, color = Cluste
### Analyse
Avec plus de clusters, on retrouve plus de précisions dans les comportements différents, avec différentes trajectoire d'expression pour les gènes qui finissent sous-exprimés et ceux qui finissent sur exprimés dans T2 et T3, et même une classe de gènes qui se sur-exprime, se calme, puis se re-sur exprime. Il est tout de même intéressant de noter que la courbe d'expression moyenne pour les gènes sur-exprimés par T1 ne bouge pas par rapport à l'analyse sur 3 clusters, il semblerait donc que ce cluster n'ait sensiblement pas bougé. On peut confirmer les tendances vues dans la première ACP, comme le fait que T1 vise des gènes qui s'expriment à un horizon temporel moyen.
Avec plus de clusters, on retrouve plus de précisions dans les comportements différents, avec différentes trajectoire d'expression pour les gènes qui finissent sous-exprimés et ceux qui finissent sur exprimés dans T2 et T3, et même une classe de gènes qui se sur-exprime, se calme, puis se re-sur exprime. Il est tout de même intéressant de noter que la courbe d'expression moyenne pour les gènes sur-exprimés par T1 ne bouge pas par rapport à l'analyse sur 3 clusters, il semblerait donc que ce cluster n'ait sensiblement pas bougé. On peut confirmer les tendances vues dans la première ACP, comme le fait que T1 vise des gènes qui s'expriment à un horizon temporel moyen.
## Question BONUS
Nous n'avons pas réussi à obtenir quelque-chose que nous étions capables d'interpréter dans la question bonus, mais elle est présente dans le Rmarkdown
```{r}
MatriceExp = T[,c(37,38,39)]
rownames(MatriceExp) = rownames(T)
@ -903,21 +904,20 @@ res_pam = pam(ds, k = 10)
# la variable de résultat ne contient pas les données originales
# Or elles sont necessaire car le champ data de fviz_cluster est utilisé
# que pour des résultats de kmeans et dbscan
pcoa_res <- cmdscale(as.matrix(ds), k = 10) # Project distance matrix to 2D
res_pam$data <- as.data.frame(pcoa_res)
res_pam$data = ds
fviz_cluster(
res_pam,
labelsize = 8, # Taille des étiquettes
geom = c("point") # Utiliser des points pour visualiser les données
labelsize = 8
)
# Visualisation des clusters dans le plan original
# visualisation des clusters dans le plan original
# Ajouter les clusters aux données d'origine
data_with_clusters <- MatriceExp
data_with_clusters$cluster <- as.factor(res_pam$clustering)
res = MatriceExp
res$cluster = as.factor(res_pam$clustering)
ggplot(data_with_clusters, aes(x = ExpT1, y = ExpT2, color = cluster)) +
ggplot(res, aes(x = ExpT1, y = ExpT2, color = cluster)) +
geom_point(size = 3) +
labs(
x = "ExpT1",
@ -925,7 +925,7 @@ ggplot(data_with_clusters, aes(x = ExpT1, y = ExpT2, color = cluster)) +
color = "Cluster"
) +
theme_minimal()
ggplot(data_with_clusters, aes(x = ExpT1, y = ExpT3, color = cluster)) +
ggplot(res, aes(x = ExpT1, y = ExpT3, color = cluster)) +
geom_point(size = 3) +
labs(
x = "ExpT1",
@ -934,7 +934,7 @@ ggplot(data_with_clusters, aes(x = ExpT1, y = ExpT3, color = cluster)) +
) +
theme_minimal()
ggplot(data_with_clusters, aes(x = ExpT2, y = ExpT3, color = cluster)) +
ggplot(res, aes(x = ExpT2, y = ExpT3, color = cluster)) +
geom_point(size = 3) +
labs(
x = "ExpT1",

724
Projet.log
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@ -1,80 +1,90 @@
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