examples/sipca-examples.R

In mixOmicsTeam/mixOmics: Omics Data Integration Project

data(liver.toxicity)

# implement IPCA on a microarray dataset
sipca.res <- sipca(liver.toxicity$gene, ncomp = 3, mode="deflation", keepX=c(50,50,50))
sipca.res

# samples representation
plotIndiv(sipca.res, ind.names = liver.toxicity$treatment[, 4],
group = as.numeric(as.factor(liver.toxicity$treatment[, 4])))

\dontrun{
plotIndiv(sipca.res, cex = 0.01, 
          col = as.numeric(as.factor(liver.toxicity$treatment[, 4])), 
          style="3d")

# variables representation
plotVar(sipca.res, cex = 2.5)

plotVar(sipca.res, rad.in = 0.5, cex = .6, style="3d")
}