--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/batch_correction_all_loess_script.R	Tue Aug 09 06:47:41 2016 -0400
@@ -0,0 +1,289 @@
+loessF <- function(datVn, qcaVi, preVi, spnN, vrbL=FALSE) {
+
+    if(length(qcaVi) < 5) {
+
+        if(vrbL)
+            cat("\nWarning: less than 5 '", refC, "'; linear regression will be performed instead of loess regression for this batch\n", sep="")
+
+        return(predict(lm(datVn[qcaVi] ~ qcaVi),
+                       newdata = data.frame(qcaVi = preVi)))
+
+    } else {
+
+        return(predict(loess(datVn[qcaVi] ~ qcaVi,
+                             control = loess.control(surface = "direct"),
+                             span = spnN),
+                       newdata = data.frame(qcaVi = preVi)))
+
+    }
+
+    ## Note:
+    ##  the surface = 'direct' argument allows extrapolation
+
+} ## loessF
+
+plotBatchF <- function(datMN, samDF.arg, spnN.arg) {
+
+    maiC <- switch(gsub("MN", "", deparse(substitute(datMN))),
+                   raw = "Raw",
+                   nrm = "Normalized")
+
+    colVc <- c(sample = "green4",
+               pool = "red",
+               blank = "black",
+               other = "yellow")
+
+    par(font = 2, font.axis = 2, font.lab = 2, lwd = 2, pch = 18)
+
+    layout(matrix(c(1, 1, 2, 3), nrow = 2),
+           widths = c(0.7, 0.3))
+
+    obsNamVc <- rownames(datMN)
+
+    obsColVc <- sapply(samDF.arg[, "sampleType"],
+                       function(typC)
+                       ifelse(typC %in% names(colVc), colVc[typC], colVc["other"]))
+
+    ## Graphic 1: Sum of intensities for each sample
+
+    par(mar = c(3.6, 3.6, 3.1, 0.6))
+
+    batTab <- table(samDF.arg[, "batch"])
+
+    sumVn <- rowSums(datMN, na.rm = TRUE)
+
+    plot(sumVn,
+         cex = 1.2,
+         col = obsColVc,
+         pch = 18,
+         xaxs = "i",
+         xlab = "",
+         ylab = "")
+
+    mtext("Injection order",
+          line = 2.2,
+          side = 1)
+    mtext("Sum of variable intensities",
+          line = 2.2,
+          side = 2)
+
+    mtext(maiC, cex = 1.2, line = 1.5, side = 3)
+
+    abline(v = cumsum(batTab) + 0.5,
+           col = "red")
+
+    mtext(names(batTab),
+          at = batTab / 2 + c(0, cumsum(batTab[-length(batTab)])))
+
+    obsColVuc <- obsColVc[sort(unique(names(obsColVc)))]
+
+    text(rep(batTab[1], times = length(obsColVuc)),
+         par("usr")[3] + (0.97 - length(obsColVuc) * 0.03 + 1:length(obsColVuc) * 0.03) * diff(par("usr")[3:4]),
+         col = obsColVuc,
+         font = 2,
+         labels = names(obsColVuc),
+         pos = 2)
+
+    for(batC in names(batTab)) {
+
+        batSeqVi <- which(samDF.arg[, "batch"] == batC)
+        batPooVi <- intersect(batSeqVi,
+                              grep("pool", samDF.arg[, "sampleType"]))
+        batSamVi <- intersect(batSeqVi,
+                              grep("sample", samDF.arg[, "sampleType"]))
+        if(length(batPooVi))
+            lines(batSeqVi,
+                  loessF(sumVn, batPooVi, batSeqVi, spnN=spnN.arg),
+                  col = colVc["pool"])
+        lines(batSeqVi,
+              loessF(sumVn, batSamVi, batSeqVi, spnN=spnN.arg),
+              col = colVc["sample"])
+
+    }
+
+    ## Graphics 2 and 3 (right): PCA score plots of components 1-4
+
+    radVn <- seq(0, 2 * pi, length.out = 100)
+    epsN <- .Machine[["double.eps"]] ## [1] 2.22e-16
+
+    pcaMN <- datMN
+
+    pcaLs <- opls(pcaMN, predI = 4, printL = FALSE, plotL = FALSE)
+    tMN <- getScoreMN(pcaLs)
+    vRelVn <- pcaLs@modelDF[, "R2X"]
+
+    n <- nrow(tMN)
+    hotN <- 2 * (n - 1) * (n^2 - 1) / (n^2 * (n - 2))
+
+    hotFisN <- hotN * qf(0.95, 2, n - 2)
+
+    pcsLs <- list(c(1, 2), c(3, 4))
+
+    par(mar = c(3.6, 3.6, 0.6, 1.1))
+
+    for(pcsN in 1:length(pcsLs)) {
+
+        pcsVn <- pcsLs[[pcsN]]
+
+        tcsMN <- tMN[, pcsVn]
+
+        micMN <- solve(cov(tcsMN))
+
+        n <- nrow(tMN)
+        hotN <- 2 * (n - 1) * (n^2 - 1) / (n^2 * (n - 2))
+
+        hotFisN <- hotN * qf(0.95, 2, n - 2)
+
+        hotVn <- apply(tcsMN,
+                       1,
+                       function(x) 1 - pf(1 / hotN * t(as.matrix(x)) %*% micMN %*% as.matrix(x), 2, n - 2))
+
+        obsHotVi <- which(hotVn < 0.05)
+
+        xLabC <- paste("t",
+                       pcsVn[1],
+                       "(",
+                       round(vRelVn[pcsVn[1]] * 100),
+                       "%)",
+                       sep = "")
+
+        yLabC <- paste("t",
+                       pcsVn[2],
+                       "(",
+                       round(vRelVn[pcsVn[2]] * 100),
+                       "%)",
+                       sep = "")
+
+        xLimVn <- c(-1, 1) * max(sqrt(var(tcsMN[, 1]) * hotFisN), max(abs(tcsMN[, 1])))
+        yLimVn <- c(-1, 1) * max(sqrt(var(tcsMN[, 2]) * hotFisN), max(abs(tcsMN[, 2])))
+
+        plot(tcsMN,
+             main = "",
+             type = "n",
+             xlab = "",
+             ylab = "",
+             xlim = xLimVn,
+             ylim = yLimVn)
+
+        mtext(xLabC,
+              line = 2.2,
+              side = 1)
+        mtext(yLabC,
+              line = 2.2,
+              side = 2)
+
+        par(lwd = 1)
+
+        abline(v = axTicks(1),
+               col = "grey")
+
+        abline(h = axTicks(2),
+               col = "grey")
+
+        abline(v = 0)
+        abline(h = 0)
+
+        lines(sqrt(var(tcsMN[, 1]) * hotFisN) * cos(radVn),
+              sqrt(var(tcsMN[, 2]) * hotFisN) * sin(radVn))
+
+        points(tcsMN,
+               col = obsColVc,
+               pch = 18)
+
+        if(length(obsHotVi))
+            text(tcsMN[obsHotVi, 1],
+                 tcsMN[obsHotVi, 2],
+                 col = obsColVc[obsHotVi],
+                 labels = obsNamVc[obsHotVi],
+                 pos = 3)
+
+    } ## for(pcsN in 1:length(pcsLs)) {
+
+    return(invisible(list(sumVn = sumVn,
+                          tcsMN = tcsMN)))
+
+} ## plotBatchF
+
+shiftBatchCorrectF <- function(rawMN.arg,
+                               samDF.arg,
+                               refC.arg,
+                               spnN.arg) {
+
+    cat("\nReference observations are: ", refC.arg, "\n")
+
+    ## computing median off all pools (or samples) for each variable
+
+    refMeaVn <- apply(rawMN.arg[samDF.arg[, "sampleType"] == refC.arg, ],
+                      2,
+                      function(feaRefVn) mean(feaRefVn, na.rm = TRUE))
+
+    ## splitting data and sample metadata from each batch
+
+    batRawLs <- split(as.data.frame(rawMN.arg),
+                      f = samDF.arg[, "batch"])
+    batRawLs <- lapply(batRawLs, function(inpDF) as.matrix(inpDF))
+
+    batSamLs <- split(as.data.frame(samDF.arg),
+                      f = samDF.arg[, "batch"])
+
+    ## checking extrapolation: are there pools at the first and last observations of each batch
+
+    if(refC.arg == "pool") {
+        pooExtML <- matrix(FALSE, nrow = 2, ncol = length(batRawLs),
+                           dimnames = list(c("first", "last"), names(batRawLs)))
+        for(batC in names(batSamLs)) {
+            batSamTypVc <- batSamLs[[batC]][, "sampleType"]
+            pooExtML["first", batC] <- head(batSamTypVc, 1) == "pool"
+            pooExtML["last", batC] <- tail(batSamTypVc, 1) == "pool"
+        }
+        if(!all(c(pooExtML))) {
+            cat("\nWarning: Pools are missing at the first and/or last position of the following batches:\n")
+            pooExtBatVi <- which(!apply(pooExtML, 2, all))
+            for(i in 1:length(pooExtBatVi))
+                cat(names(pooExtBatVi)[i], ": ",
+                    paste(rownames(pooExtML)[!pooExtML[, pooExtBatVi[i]]], collapse = ", "), "\n", sep = "")
+            cat("Extrapolating loess fits for these batches may result in inaccurate modeling!\n")
+        }
+    }
+
+    ## normalizing
+
+    nrmMN <- NULL ## normalized data matrix to be computed
+
+    cat("\nProcessing batch:")
+
+    for(batC in names(batRawLs)) { ## processing each batch individually
+
+        cat("\n", batC)
+
+        batRawMN <- batRawLs[[batC]]
+        batSamDF <- batSamLs[[batC]]
+
+        batAllVi <- 1:nrow(batRawMN)
+
+        batRefVi <- grep(refC.arg, batSamDF[, "sampleType"])
+
+        ## prediction of the loess fit
+
+        batLoeMN <- apply(batRawMN,
+                          2,
+                          function(rawVn) loessF(rawVn, batRefVi, batAllVi, spnN=spnN.arg, vrbL=TRUE))
+
+        ## normalization
+
+        batLoeMN[batLoeMN <= 0] <- NA
+
+        batNrmMN <- batRawMN / batLoeMN
+
+        nrmMN <- rbind(nrmMN,
+                       batNrmMN)
+
+    }
+
+    cat("\n")
+
+    nrmMN <- sweep(nrmMN, MARGIN = 2, STATS = refMeaVn, FUN = "*")
+
+    return(nrmMN)
+
+} ## shiftBatchCorrectF