## ---- echo = FALSE, results = "asis"-------------------------------------
options(width = 130)
BiocStyle::markdown()
set.seed(44)

## ---- message = FALSE----------------------------------------------------
library(ClassifyR)
library(ggplot2)
library(curatedOvarianData)
data(GSE26712_eset)
GSE26712_eset <- GSE26712_eset[1:1000, ]

## ---- results = "hold", tidy = FALSE-------------------------------------
curatedClinical <- pData(GSE26712_eset)
ovarPoor <- curatedClinical[, "vital_status"] == "deceased" & curatedClinical[, "days_to_death"] < 365 * 1
ovarGood <- curatedClinical[, "vital_status"] == "living" & curatedClinical[, "days_to_death"] > 365 * 5
sum(ovarPoor, na.rm = TRUE)
sum(ovarGood, na.rm = TRUE)

## ------------------------------------------------------------------------
ovarExpression <- exprs(GSE26712_eset)[, c(which(ovarPoor), which(ovarGood))]
ovarGroups <- factor(rep(c("Poor", "Good"), c(length(which(ovarPoor)), length(which(ovarGood)))),
                     levels = c("Poor", "Good"))

## ---- fig.width = 18, fig.height = 10, tidy = FALSE----------------------
plotData <- data.frame(expression = as.numeric(ovarExpression),
                       sample = factor(rep(1:ncol(ovarExpression), each = nrow(ovarExpression))))

ggplot(plotData, aes(x = sample, y = expression)) + geom_boxplot() +
       scale_y_continuous(limits = c(0, 15)) + xlab("Sample") + ylab("Expression Value") +
       ggtitle("Expression for All Arrays") 

## ---- tidy = FALSE-------------------------------------------------------
groupsTable <- data.frame(class = ovarGroups)
rownames(groupsTable) <- colnames(ovarExpression)
ovarSet <- ExpressionSet(ovarExpression, AnnotatedDataFrame(groupsTable))
featureNames(ovarSet) <- rownames(ovarExpression)
dim(ovarSet)

## ---- tidy = FALSE-------------------------------------------------------
library(sparsediscrim)
DEresults <- runTests(ovarSet, "Ovarian Cancer", "Differential Expression", validation = "bootstrap", resamples = 5, folds = 3,
                      params = list(SelectParams(limmaSelection, resubstituteParams = ResubstituteParams(nFeatures = c(25, 50, 75, 100), performanceType = "balanced", better = "lower")),
                                    TrainParams(dlda, TRUE, doesTests = FALSE),
                                    PredictParams(predict, TRUE, getClasses = function(result) result[["class"]])),
                      parallelParams = bpparam(), verbose = 1)
DEresults

## ---- fig.height = 12, fig.width = 12, results = "hold", message = FALSE----
DEplots <- plotFeatureClasses(ovarSet, features(DEresults)[[1]][[2]][1:5])

## ------------------------------------------------------------------------
DEresults <- calcPerformance(DEresults, "balanced")
DEresults
performance(DEresults)

## ------------------------------------------------------------------------
DEresults <- calcPerformance(DEresults, "mat")
DEresults
performance(DEresults)

## ---- tidy = FALSE-------------------------------------------------------
DVresults <- runTests(ovarSet, "Ovarian Cancer", "Differential Variability",
                      validation = "bootstrap", resamples = 2, folds = 4,
                      params = list(SelectParams(leveneSelection, resubstituteParams = ResubstituteParams(nFeatures = c(25, 50, 75, 100), performanceType = "balanced", better = "lower")),
                                    TransformParams(subtractFromLocation, location = "median"),
                                    TrainParams(fisherDiscriminant, FALSE, doesTests = TRUE),
                                    PredictParams(predictor = function(){}, FALSE, getClasses = function(result) result, returnType = "both")),
                      verbose = 1)
DVresults

## ---- fig.height = 12, fig.width = 12, results = "hold", message = FALSE----
DVplots <- plotFeatureClasses(ovarSet, features(DVresults)[[1]][[2]][1:5])

## ------------------------------------------------------------------------
DVresults <- calcPerformance(DVresults, "balanced")
DVresults
performance(DVresults)

## ---- tidy = FALSE-------------------------------------------------------
dParams <- list(bw = "nrd0", n = 4096, from = expression(min(featureValues)),
                to = expression(max(featureValues)))
DDresults <- runTests(ovarSet, "Ovarian Cancer", "Differential Distribution",
                      validation = "bootstrap", resamples = 2, folds = 2,
                      params = list(SelectParams(KullbackLeiblerSelection, resubstituteParams = ResubstituteParams(nFeatures = c(25, 50, 75, 100), performanceType = "balanced", better = "lower")),
                                    TrainParams(naiveBayesKernel, FALSE, doesTests = TRUE),
                                    PredictParams(predictor = function(){}, FALSE, getClasses = function(result) result, weighted = "weighted", returnType = "both",
                                                  densityParameters = dParams)),
                                verbose = 1)
DDresults

## ---- fig.height = 12, fig.width = 12, results = "hold", message = FALSE----
DDplots <- plotFeatureClasses(ovarSet, features(DDresults[[1]])[[1]][[1]][1:5])

## ------------------------------------------------------------------------
DDresults[["weight=crossover distance"]] <- calcPerformance(DDresults[["weight=crossover distance"]], "balanced")
DDresults[["weight=crossover distance"]]
performance(DDresults[["weight=crossover distance"]])

## ---- fig.width = 10, fig.height = 7-------------------------------------
library(grid)
resultsList <- list(Expression = DEresults, Variability = DVresults)
errorPlot <- errorMap(resultsList)

## ---- fig.width = 6.8, fig.height = 5------------------------------------
errorBoxes <- performancePlot(list(DEresults, DVresults, DDresults[["weight=crossover distance"]]),
                              performanceName = "Balanced Error Rate",
                              boxFillColouring  = "None", boxLineColouring = "None",
                              title = "Errors Across Classification Types")

## ------------------------------------------------------------------------
trainingExpr <- matrix(rnorm(500 * 50, 9, 3), ncol = 50)
trainingClasses <- factor(rep(c("Healthy", "Diseased"), each = 25), levels = c("Healthy", "Diseased"))
trainingExpr[101:125, trainingClasses == "Diseased"] <- trainingExpr[101:125, trainingClasses == "Diseased"] - 2

testingExpr <- matrix(rnorm(500 * 50, 9, 3), ncol = 50)
testingClasses <- factor(rep(c("Healthy", "Diseased"), each = 25), levels = c("Healthy", "Diseased"))
testingExpr[111:135, testingClasses == "Diseased"] <- testingExpr[111:135, testingClasses == "Diseased"] - 2

## ------------------------------------------------------------------------
allExpr <- cbind(trainingExpr, testingExpr)
allClasses <- unlist(list(trainingClasses, testingClasses))
independentResult  <- runTest(allExpr, allClasses, datasetName = "Simulation", classificationName = "DE",
                              training = 1:50, testing = 51:100)
independentResult

## ---- fig.height = 5, fig.width = 6--------------------------------------
ROCcurves <- ROCplot(list(DVresults, DDresults[["weight=crossover distance"]]))

## ------------------------------------------------------------------------
library(e1071) # Provides SVM functions.
resubstituteParams = ResubstituteParams(nFeatures = c(25, 50, 75, seq(100, 1000, 100)), performanceType = "balanced", better = "lower")
SVMresults <- suppressWarnings(runTests(ovarSet, "Ovarian Cancer", "Differential Expression", validation = "bootstrap", resamples = 5, folds = 3,
                      params = list(SelectParams(limmaSelection, resubstituteParams = resubstituteParams),
                                    TrainParams(svm, TRUE, doesTests = FALSE, kernel = "linear", resubstituteParams = resubstituteParams, tuneParams = list(cost = c(0.01, 0.1, 1, 10))),
                                    PredictParams(predict, TRUE, getClasses = function(result) result)),
                      parallelParams = bpparam(), verbose = 1))

## ------------------------------------------------------------------------
length(tunedParameters(SVMresults))
tunedParameters(SVMresults)[[1]]