mouse=read.table("http://factominer.free.fr/more/souris.csv",header=T,sep=";",row.names=1) ## setwd("D:/Documents and Settings/Husson/Bureau/ecole doctorale") ## mouse=read.table("souris.csv",header=T,sep=";",row.names=1) #The data set contains: ##1 variable qualitative de genotype : W and NW ##1 variable qualitative de regime : dha, efad, lin, ref and tournesol ##21 concentrations d'acides gras ##120 expressions de genes ################################## ## ACP sur les acides gras ## ################################## library(FactoMineR) res.pca<-PCA(mouse,quali.sup=1:2,quanti.sup=24:ncol(mouse)) barplot(res.pca$eig[,1],main="Valeurs propres",names.arg=1:nrow(res.pca$eig)) dimdesc(res.pca) plot.PCA(res.pca,habillage=2,invisible="quali") plot.PCA(res.pca,habillage=1,invisible="quali") plotellipses(res.pca) plotellipses(res.pca,keepvar="Regime") ################################## ## ACP sur les gènes ## ################################## res.pca.genes<-PCA(mouse,quanti.sup=3:23,quali.sup=1:2) dimdesc(res.pca.genes) plot.PCA(res.pca.genes,habillage=2,invisible="quali") plot.PCA(res.pca.genes,habillage=1,invisible="quali") plotellipses(res.pca.genes) res.hcpc = HCPC(res.pca) res.hcpc ################################## #### AFM #### ################################## res.mfa<-MFA(mouse,group=c(2,21,120),type=c("n","s","s"),num.group.sup=1,name.group=c("Régime-gène-Geno","Acide gras","Gene")) barplot(res.mfa$eig[,1],main="Valeurs propres",names.arg=1:nrow(res.pca$eig)) dimdesc(res.mfa) plot.MFA(res.mfa2,choix="var",) plotellipses(res.mfa,keepvar="Regime") plotellipses(res.mfa,keepvar="Genotype") plot.MFA(res.mfa,choix="ind",invisible="quali",partial="all",habillage="group")