#analysis library(ade4) library(ggplot2) library(reshape2) library(gridExtra) data(alimintestData) data(basal_diet)
metadata76 = alimintestData$metadata metadata76$Time.point = as.factor(metadata76$Time.point) basal_diet_tmp = basal_diet[which(basal_diet$visite=="before_study"),] for(i in 4:dim(basal_diet_tmp)[2]){ basal_diet_tmp[,i] = as.factor(as.character(basal_diet_tmp[,i])) } diet.acm = dudi.acm(basal_diet_tmp[,-c(1:3)], nf=3, scannf=FALSE) diet.bca = bca(diet.acm, fac=as.factor(basal_diet_tmp[,1]), nf=3, scannf=F) #randtest(diet.bca) basal_richness = metadata76[which(metadata76$Time.point=="2"),c("Subject_Id","richness")] diet.richness.bca = merge(data.frame(Subject_Id=row.names(diet.bca$li), diet.bca$li), basal_richness, by="Subject_Id") #diet.bca$co[order(diet.bca$co[,3]+diet.bca$co[,2]),] diet.richness.bca2 = merge(data.frame(diet.bca$ls, Subject_Id=basal_diet_tmp[,1]),diet.richness.bca, by= "Subject_Id")
p1_diet = ggplot(diet.richness.bca2) + geom_point(aes(x=CS2,y=CS3)) + geom_segment(aes(x=CS2,y=CS3, xend=Axis2, yend=Axis3, col=Subject_Id)) + geom_text(aes(x=Axis2, y=Axis3, label=Subject_Id)) + xlab("PC2") +ylab("PC3") + guides(col=FALSE) p2_diet = ggplot(diet.richness.bca, aes(x=Axis2+Axis3, y=richness, col=richness)) + geom_point(size=4) + xlab("PC2 + PC3") + ylab("Microbiota richness") grid.arrange(p1_diet,p2_diet, ncol=2)
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