examples/spls-examples.R

In mixOmicsTeam/mixOmics: Omics Data Integration Project

data(liver.toxicity)
X <- liver.toxicity$gene
Y <- liver.toxicity$clinic

toxicity.spls <- spls(X, Y, ncomp = 2, keepX = c(50, 50),
keepY = c(10, 10))

toxicity.spls <- spls(X, Y[,1:2,drop=FALSE], ncomp = 5, keepX = c(50, 50))#,  mode="canonical")

\dontrun{

## Second example: one-factor multilevel analysis with sPLS, selecting a subset of variables
#--------------------------------------------------------------

data(liver.toxicity)
# note: we made up those data, pretending they are repeated measurements
repeat.indiv <- c(1, 2, 1, 2, 1, 2, 1, 2, 3, 3, 4, 3, 4, 3, 4, 4, 5, 6, 5, 5,
6, 5, 6, 7, 7, 8, 6, 7, 8, 7, 8, 8, 9, 10, 9, 10, 11, 9, 9,
10, 11, 12, 12, 10, 11, 12, 11, 12, 13, 14, 13, 14, 13, 14,
13, 14, 15, 16, 15, 16, 15, 16, 15, 16)
summary(as.factor(repeat.indiv)) # 16 rats, 4 measurements each

# this is a spls (unsupervised analysis) so no need to mention any factor in design
# we only perform a one level variation split
design <- data.frame(sample = repeat.indiv)
res.spls.1level <- spls(X = liver.toxicity$gene,
Y=liver.toxicity$clinic,
multilevel = design,
ncomp = 3,
keepX = c(50, 50, 50), keepY = c(5, 5, 5),
mode = 'canonical')

# set up colors and pch for plotIndiv
col.stimu <- 1:nlevels(design$stimu)

plotIndiv(res.spls.1level, rep.space = 'X-variate', ind.names = FALSE,
group = liver.toxicity$treatment$Dose.Group,
pch = 20, main = 'Gene expression subspace',
legend = TRUE)


plotIndiv(res.spls.1level, rep.space = 'Y-variate', ind.names = FALSE,
group = liver.toxicity$treatment$Dose.Group,
pch = 20, main = 'Clinical measurements ssubpace',
legend = TRUE)

plotIndiv(res.spls.1level, rep.space = 'XY-variate', ind.names = FALSE,
group = liver.toxicity$treatment$Dose.Group,
pch = 20, main = 'Both Gene expression and Clinical subspaces',
legend = TRUE)

## Third example: two-factor multilevel analysis with sPLS, selecting a subset of variables
#--------------------------------------------------------------

data(liver.toxicity)
dose <- as.factor(liver.toxicity$treatment$Dose.Group)
time <- as.factor(liver.toxicity$treatment$Time.Group)
# note: we made up those data, pretending they are repeated measurements
repeat.indiv <- c(1, 2, 1, 2, 1, 2, 1, 2, 3, 3, 4, 3, 4, 3, 4, 4, 5, 6, 5, 5,
6, 5, 6, 7, 7, 8, 6, 7, 8, 7, 8, 8, 9, 10, 9, 10, 11, 9, 9,
10, 11, 12, 12, 10, 11, 12, 11, 12, 13, 14, 13, 14, 13, 14,
13, 14, 15, 16, 15, 16, 15, 16, 15, 16)
summary(as.factor(repeat.indiv)) # 16 rats, 4 measurements each
design <- data.frame(sample = repeat.indiv, dose = dose, time = time)

res.spls.2level = spls(liver.toxicity$gene,
Y = liver.toxicity$clinic,
multilevel = design,
ncomp=2,
keepX = c(10,10), keepY = c(5,5))
}