examples/predict-examples.R

In mixOmicsTeam/mixOmics: Omics Data Integration Project

data(linnerud)
X <- linnerud$exercise
Y <- linnerud$physiological
linn.pls <- pls(X, Y, ncomp = 2, mode = "classic")

indiv1 <- c(200, 40, 60)
indiv2 <- c(190, 45, 45)
newdata <- rbind(indiv1, indiv2)
colnames(newdata) <- colnames(X)
newdata

pred <- predict(linn.pls, newdata)

plotIndiv(linn.pls, comp = 1:2, rep.space = "X-variate",style="graphics",ind.names=FALSE)
points(pred$variates[, 1], pred$variates[, 2], pch = 19, cex = 1.2)
text(pred$variates[, 1], pred$variates[, 2],
c("new ind.1", "new ind.2"), pos = 3)

## First example with plsda
data(liver.toxicity)
X <- liver.toxicity$gene
Y <- as.factor(liver.toxicity$treatment[, 4])


## if training is perfomed on 4/5th of the original data
samp <- sample(1:5, nrow(X), replace = TRUE)
test <- which(samp == 1)   # testing on the first fold
train <- setdiff(1:nrow(X), test)

plsda.train <- plsda(X[train, ], Y[train], ncomp = 2)
test.predict <- predict(plsda.train, X[test, ], dist = "max.dist")
Prediction <- test.predict$class$max.dist[, 2]
cbind(Y = as.character(Y[test]), Prediction)

\dontrun{
## Second example with splsda
splsda.train <- splsda(X[train, ], Y[train], ncomp = 2, keepX = c(30, 30))
test.predict <- predict(splsda.train, X[test, ], dist = "max.dist")
Prediction <- test.predict$class$max.dist[, 2]
cbind(Y = as.character(Y[test]), Prediction)


## example with block.splsda=diablo=sgccda and a missing block
data(nutrimouse)
# need to unmap Y for an unsupervised analysis, where Y is included as a data block in data
Y.mat = unmap(nutrimouse$diet)
data = list(gene = nutrimouse$gene, lipid = nutrimouse$lipid, Y = Y.mat)
# with this design, all blocks are connected
design = matrix(c(0,1,1,1,0,1,1,1,0), ncol = 3, nrow = 3,
byrow = TRUE, dimnames = list(names(data), names(data)))

# train on 75% of the data
ind.train=NULL
for(i in 1:nlevels(nutrimouse$diet))
ind.train=c(ind.train,which(nutrimouse$diet==levels(nutrimouse$diet)[i])[1:6])

#training set
gene.train=nutrimouse$gene[ind.train,]
lipid.train=nutrimouse$lipid[ind.train,]
Y.mat.train=Y.mat[ind.train,]
Y.train=nutrimouse$diet[ind.train]
data.train=list(gene=gene.train,lipid=lipid.train,Y=Y.mat.train)

#test set
gene.test=nutrimouse$gene[-ind.train,]
lipid.test=nutrimouse$lipid[-ind.train,]
Y.mat.test=Y.mat[-ind.train,]
Y.test=nutrimouse$diet[-ind.train]
data.test=list(gene=gene.test,lipid=lipid.test)

# example with block.splsda=diablo=sgccda and a missing block
res.train = block.splsda(X=list(gene=gene.train,lipid=lipid.train),Y=Y.train,
ncomp=3,keepX=list(gene=c(10,10,10),lipid=c(5,5,5)))
test.predict = predict(res.train, newdata=data.test[2], method = "max.dist")


## example with mint.splsda
data(stemcells)

#training set
ind.test = which(stemcells$study == "3")
gene.train = stemcells$gene[-ind.test,]
Y.train = stemcells$celltype[-ind.test]
study.train = factor(stemcells$study[-ind.test])

#test set
gene.test = stemcells$gene[ind.test,]
Y.test = stemcells$celltype[ind.test]
study.test = factor(stemcells$study[ind.test])

res = mint.splsda(X = gene.train, Y = Y.train, ncomp = 3, keepX = c(10, 5, 15),
study = study.train)

pred = predict(res, newdata = gene.test, study.test = study.test)

data.frame(Truth = Y.test, prediction = pred$class$max.dist)

}