examples/splsda-examples.R

In mixOmicsTeam/mixOmics: Omics Data Integration Project

## First example
data(breast.tumors)
X <- breast.tumors$gene.exp
# Y will be transformed as a factor in the function,
# but we set it as a factor to set up the colors.
Y <- as.factor(breast.tumors$sample$treatment)

res <- splsda(X, Y, ncomp = 2, keepX = c(25, 25))


# individual names appear
plotIndiv(res, ind.names = Y, legend = TRUE, ellipse =TRUE)

\dontrun{
## Second example: one-factor analysis with sPLS-DA, selecting a subset of variables
# as in the paper Liquet et al.
#--------------------------------------------------------------
data(vac18)
X <- vac18$genes
Y <- vac18$stimulation
# sample indicates the repeated measurements
design <- data.frame(sample = vac18$sample)
Y = data.frame(stimul = vac18$stimulation)

# multilevel sPLS-DA model
res.1level <- splsda(X, Y = Y, ncomp = 3, multilevel = design,
keepX = c(30, 137, 123))

# set up colors for plotIndiv
col.stim <- c("darkblue", "purple", "green4","red3")
plotIndiv(res.1level, ind.names = Y, col.per.group = col.stim)

## Third example: two-factor analysis with sPLS-DA, selecting a subset of variables
# as in the paper Liquet et al.
#--------------------------------------------------------------

data(vac18.simulated) # simulated data

X <- vac18.simulated$genes
design <- data.frame(sample = vac18.simulated$sample)
Y = data.frame( stimu = vac18.simulated$stimulation,
time = vac18.simulated$time)

res.2level <- splsda(X, Y = Y, ncomp = 2, multilevel = design,
keepX = c(200, 200))

plotIndiv(res.2level, group = Y$stimu, ind.names = vac18.simulated$time,
legend = TRUE, style = 'lattice')



## Fourth example: with more than two classes
# ------------------------------------------------

data(liver.toxicity)
X <- as.matrix(liver.toxicity$gene)
# Y will be transformed as a factor in the function,
# but we set it as a factor to set up the colors.
Y <- as.factor(liver.toxicity$treatment[, 4])

splsda.liver <- splsda(X, Y, ncomp = 2, keepX = c(20, 20))

# individual name is set to the treatment
plotIndiv(splsda.liver, ind.names = Y, ellipse = TRUE, legend = TRUE)


## Fifth example: 16S data with multilevel decomposion and log ratio transformation
# ------------------------------------------------

data(diverse.16S)
splsda.16S = splsda(
X = diverse.16S$data.TSS,  # TSS normalised data
Y =  diverse.16S$bodysite,
multilevel = diverse.16S$sample, # multilevel decomposition
ncomp = 2,
keepX =  c(10, 150),
logratio= 'CLR')  # CLR log ratio transformation


plotIndiv(splsda.16S, ind.names = FALSE, pch = 16, ellipse = TRUE, legend = TRUE)
#OTUs selected at the family level
diverse.16S$taxonomy[selectVar(splsda.16S, comp = 1)$name,'Family']
}