examples/spca-examples.R

In mixOmicsTeam/mixOmics: Omics Data Integration Project

data(liver.toxicity)
spca.rat <- spca(liver.toxicity$gene, ncomp = 3, keepX = rep(50, 3))
spca.rat

## variable representation
plotVar(spca.rat, cex = 1)
\dontrun{
plotVar(spca.rat,style="3d")
}

## samples representation
plotIndiv(spca.rat, ind.names = liver.toxicity$treatment[, 3],
          group = as.numeric(liver.toxicity$treatment[, 3]))

\dontrun{
plotIndiv(spca.rat, cex = 0.01,
col = as.numeric(liver.toxicity$treatment[, 3]),style="3d")
}

## example with multilevel decomposition and CLR log ratio transformation
data("diverse.16S")
spca.res = spca(X = diverse.16S$data.TSS, ncomp = 5,
logratio = 'CLR', multilevel = diverse.16S$sample)
plot(spca.res)
plotIndiv(spca.res, ind.names = FALSE, group = diverse.16S$bodysite, title = '16S diverse data',
legend=TRUE)