archive/ConsensusClusterPlus_1.R

In Gibbsdavidl/ConsensusClusterParallelPlus: ConsensusClusterPlus

ConsensusClusterParallelPlus <- function(d = NULL, maxK = 3, reps = 10, cores = 1,
    pItem = 0.8, pFeature = 1, clusterAlg = "hc", title = "untitled_consensus_cluster",
    innerLinkage = "average", finalLinkage = "average", distance = "pearson", ml = NULL,
    tmyPal = NULL, seed = NULL, plot = NULL, writeTable = FALSE, weightsItem = NULL,
    weightsFeature = NULL, verbose = F, corUse = "everything") {
    ## description: runs consensus subsamples
    require(fastcluster)

    if (is.null(seed) == TRUE) {
        seed = timeSeed = as.numeric(Sys.time())
    }
    set.seed(seed)

    # distance=ifelse( inherits(d,'dist'), attr( d, 'method' ), 'pearson' )


    if (is.null(ml) == TRUE) {

        if (!class(d) %in% c("dist", "matrix", "ExpressionSet")) {
            stop("d must be a matrix, distance object or ExpressionSet (eset object)")
        }

        if (inherits(d, "dist")) {
            ## if d is a distance matrix, fix a few things so that they don't cause problems
            ## with the analysis Note, assumption is that if d is a distance matrix, the user
            ## doesn't want to sample over the row features
            if (is.null(attr(d, "method"))) {
                attr(d, "method") <- distance <- "unknown - user-specified"
            }
            if (is.null(distance) || (distance != attr(d, "method"))) {
                distance <- attr(d, "method")
            }

            if ((!is.null(pFeature)) && (pFeature < 1)) {
                message("Cannot use the pFeatures parameter when specifying a distance matrix as the data object\n")
                pFeature <- 1
            }
            if (!is.null(weightsFeature)) {
                message("Cannot use the weightsFeature parameter when specifying a distance matrix as the data object\n")
                weightsFeature <- NULL
            }
            if (clusterAlg == "km") {
                message("Note: k-means will cluster the distance matrix you provided.  This is similar to kmdist option when suppling a data matrix")
                ## d <- as.matrix( d ) #this is now done w/in ccRun
            }
        } else {
            if (is.null(distance)) {
                ## we should never get here, but just in case
                distance <- "pearson"
            }
        }

        if ((clusterAlg == "km") && inherits(distance, "character") && (distance !=
            "euclidean")) {
            message("Note: The km (kmeans) option only supports a euclidean distance metric when supplying a data matrix.  If you want to cluster a distance matrix using k-means use the 'kmdist' option, or use a different algorithm such as 'hc' or 'pam'.  Changing distance to euclidean")
            distance <- "euclidean"
        }


        if (inherits(d, "ExpressionSet")) {
            d <- exprs(d)
        }

        ml <- ccRun(d = d, maxK = maxK, repCount = reps, coreCount = cores, diss = inherits(d,
            "dist"), pItem = pItem, pFeature = pFeature, innerLinkage = innerLinkage,
            clusterAlg = clusterAlg, weightsFeature = weightsFeature, weightsItem = weightsItem,
            distance = distance, verbose = verbose, corUse = corUse)

    }
    res = list()

    ## make results directory
    if ((is.null(plot) == FALSE | writeTable) & !file.exists(paste(title, sep = ""))) {
        dir.create(paste(title, sep = ""))
    }

    ## write log file
    log <- matrix(ncol = 2, byrow = T, c("title", title, "maxK", maxK, "input matrix rows",
        ifelse(inherits(d, "matrix"), nrow(d), "dist-mat"), "input matrix columns",
        ifelse(inherits(d, "matrix"), ncol(d), ncol(as.matrix(d))), "number of bootstraps",
        reps, "item subsampling proportion", pItem, "feature subsampling proportion",
        ifelse(is.null(pFeature), 1, pFeature), "cluster algorithm", clusterAlg,
        "inner linkage type", innerLinkage, "final linkage type", finalLinkage, "correlation method",
        distance, "plot", if (is.null(plot)) NA else plot, "seed", if (is.null(seed)) NA else seed))
    colnames(log) = c("argument", "value")
    if (writeTable) {
        write.csv(file = paste(title, "/", title, ".log.csv", sep = ""), log, row.names = F)
    }
    if (is.null(plot)) {
        ## nothing
    } else if (plot == "pngBMP") {
        bitmap(paste(title, "/", "consensus%03d.png", sep = ""))
    } else if (plot == "png") {
        png(paste(title, "/", "consensus%03d.png", sep = ""))

    } else if (plot == "pdf") {
        pdf(onefile = TRUE, paste(title, "/", "consensus.pdf", sep = ""))
    } else if (plot == "ps") {
        postscript(onefile = TRUE, paste(title, "/", "consensus.ps", sep = ""))
    }

    colorList = list()
    colorM = rbind()  #matrix of colors.

    # 18 colors for marking different clusters
    thisPal <- c("#A6CEE3", "#1F78B4", "#B2DF8A", "#33A02C", "#FB9A99", "#E31A1C",
        "#FDBF6F", "#FF7F00", "#CAB2D6", "#6A3D9A", "#FFFF99", "#B15928", "#bd18ea",
        "#2ef4ca", "#f4cced", "#f4cc03", "#05188a", "#e5a25a", "#06f106", "#85848f",
        "#000000", "#076f25", "#93cd7f", "#4d0776", "#ffffff")

    ## plot scale
    colBreaks = NA
    if (is.null(tmyPal) == TRUE) {
        colBreaks = 10
        tmyPal = myPal(colBreaks)
    } else {
        colBreaks = length(tmyPal)
    }
    sc = cbind(seq(0, 1, by = 1/(colBreaks)))
    rownames(sc) = sc[, 1]
    sc = cbind(sc, sc)
    heatmap(sc, Colv = NA, Rowv = NA, symm = FALSE, scale = "none", col = tmyPal,
        na.rm = TRUE, labRow = rownames(sc), labCol = F, main = "consensus matrix legend")

    for (tk in 2:maxK) {
        if (verbose) {
            message(paste("consensus ", tk))
        }
        fm = ml[[tk]]
        hc = fastcluster::hclust(as.dist(1 - fm), method = finalLinkage)
        message("clustered")
        ct = cutree(hc, tk)
        names(ct) = colnames(d)
        if (class(d) == "dist") {
            names(ct) = colnames(as.matrix(d))
        }
        c = fm

        colorList = setClusterColors(res[[tk - 1]][[3]], ct, thisPal, colorList)
        pc = c
        pc = pc[hc$order, ]  #pc is matrix for plotting, same as c but is row-ordered and has names and extra row of zeros.

        if (!is.null(plot) && plot == "pngBMP") {
            pc = pc[, hc$order]  #mod for no tree
            pc = rbind(pc, 0)
            # no dendrogram if pngBMP
            oc = colorList[[1]][hc$order]  #mod for no tree
            heatmap(pc, Colv = NA, Rowv = NA, symm = FALSE, scale = "none", col = tmyPal,
                na.rm = TRUE, labRow = F, labCol = F, mar = c(5, 5), main = paste("consensus matrix k=",
                  tk, sep = ""), ColSideCol = oc)
        } else {
            pc = rbind(pc, 0)
            # former with tree:
            heatmap(pc, Colv = as.dendrogram(hc), Rowv = NA, symm = FALSE, scale = "none",
                col = tmyPal, na.rm = TRUE, labRow = F, labCol = F, mar = c(5, 5),
                main = paste("consensus matrix k=", tk, sep = ""), ColSideCol = colorList[[1]])
        }

        legend("topright", legend = unique(ct), fill = unique(colorList[[1]]), horiz = FALSE)

        res[[tk]] = list(consensusMatrix = c, consensusTree = hc, consensusClass = ct,
            ml = ml[[tk]], clrs = colorList)
        colorM = rbind(colorM, colorList[[1]])
    }
    CDF(ml)
    clusterTrackingPlot(colorM[, res[[length(res)]]$consensusTree$order])
    if (is.null(plot) == FALSE) {
        dev.off()
    }
    res[[1]] = colorM
    if (writeTable) {
        for (i in 2:length(res)) {
            write.csv(file = paste(title, "/", title, ".k=", i, ".consensusMatrix.csv",
                sep = ""), res[[i]]$consensusMatrix)
            write.table(file = paste(title, "/", title, ".k=", i, ".consensusClass.csv",
                sep = ""), res[[i]]$consensusClass, col.names = F, sep = ",")
        }
    }
    return(res)
}


calcICL = function(res, title = "untitled_consensus_cluster", plot = NULL, writeTable = FALSE) {
    # calculates and plots cluster consensus and item consensus
    cc = rbind()
    cci = rbind()
    sumRes = list()
    colorsArr = c()

    # make results directory
    if ((is.null(plot) == FALSE | writeTable) & !file.exists(paste(title, sep = ""))) {
        dir.create(paste(title, sep = ""))
    }
    if (is.null(plot)) {
        # to screen
    } else if (plot == "pdf") {
        pdf(onefile = TRUE, paste(title, "/", "icl.pdf", sep = ""))
    } else if (plot == "ps") {
        postscript(onefile = TRUE, paste(title, "/", "icl.ps", sep = ""))
    } else if (plot == "png") {
        png(paste(title, "/", "icl%03d.png", sep = ""))
    } else if (plot == "pngBMP") {
        bitmap(paste(title, "/", "icl%03d.png", sep = ""))
    }

    par(mfrow = c(3, 1), mar = c(4, 3, 2, 0))

    for (k in 2:length(res)) {
        # each k
        eiCols = c()
        o = res[[k]]
        m = o$consensusMatrix
        m = triangle(m, mode = 2)
        for (ci in sort(unique(o$consensusClass))) {
            # each cluster in k
            items = which(o$consensusClass == ci)
            nk = length(items)
            mk = sum(m[items, items], na.rm = T)/((nk * (nk - 1))/2)
            cc = rbind(cc, c(k, ci, mk))  #cluster-consensus

            for (ei in rev(res[[2]]$consensusTree$order)) {
                denom = if (ei %in% items) {
                  nk - 1
                } else {
                  nk
                }
                mei = sum(c(m[ei, items], m[items, ei]), na.rm = T)/denom  # mean item consensus to a cluster.
                cci = rbind(cci, c(k, ci, ei, mei))  #cluster, cluster index, item index, item-consensus
            }
            eiCols = c(eiCols, rep(ci, length(o$consensusClass)))
        }

        cck = cci[which(cci[, 1] == k), ]  #only plot the new k data.

        # group by item, order by cluster i
        w = lapply(split(cck, cck[, 3]), function(x) {
            y = matrix(unlist(x), ncol = 4)
            y[order(y[, 2]), 4]
        })
        q = matrix(as.numeric(unlist(w)), ncol = length(w), byrow = F)
        q = q[, res[[2]]$consensusTree$order]  #order by leave order of k=2
        # q is a matrix of k rows and sample columns, values are item consensus of sample
        # to the cluster.

        thisColors = unique(cbind(res[[k]]$consensusClass, res[[k]]$clrs[[1]]))
        thisColors = thisColors[order(as.numeric(thisColors[, 1])), 2]
        colorsArr = c(colorsArr, thisColors)
        sumRes[[k]] = rankedBarPlot(q, thisColors, cc = res[[k]]$consensusClass[res[[2]]$consensusTree$order],
            paste("k=", k, sep = ""))
    }

    ys = cs = lab = c()
    lastk = cc[1, 1]
    for (i in 1:length(colorsArr)) {
        if (lastk != cc[i, 1]) {
            ys = c(ys, 0, 0)
            cs = c(cs, NA, NA)
            lastk = cc[i, 1]
            lab = c(lab, NA, NA)
        }
        ys = c(ys, cc[i, 3])
        cs = c(cs, colorsArr[i])
        lab = c(lab, cc[i, 1])
    }
    names(ys) = lab
    par(mfrow = c(3, 1), mar = c(4, 3, 2, 0))
    barplot(ys, col = cs, border = cs, main = "cluster-consensus", ylim = c(0, 1),
        las = 1)
    if (is.null(plot) == FALSE) {
        dev.off()
    }
    colnames(cc) = c("k", "cluster", "clusterConsensus")
    colnames(cci) = c("k", "cluster", "item", "itemConsensus")
    cci[, "item"] = names(res[[2]]$consensusClass)[cci[, "item"]]
    # type cci
    cci = data.frame(k = as.numeric(cci[, "k"]), cluster = as.numeric(cci[, "cluster"]),
        item = cci[, "item"], itemConsensus = as.numeric(cci[, "itemConsensus"]))

    # write to file.
    if (writeTable) {
        write.csv(file = paste(title, "/", title, ".summary.cluster.consensus.csv",
            sep = ""), row.names = F, cc)
        write.csv(file = paste(title, "/", title, ".summary.item.consensus.csv",
            sep = ""), row.names = F, cc)
    }
    return(list(clusterConsensus = cc, itemConsensus = cci))
}


ccRun <- function(d = d, maxK = NULL, repCount = NULL, coreCount = NULL, diss = inherits(d,
    "dist"), pItem = NULL, pFeature = NULL, innerLinkage = NULL, distance = NULL,
    clusterAlg = NULL, weightsItem = NULL, weightsFeature = NULL, verbose = NULL,
    corUse = NULL) {
    m = vector(mode = "list", repCount)
    ml = vector(mode = "list", maxK)

    n <- ifelse(diss, ncol(as.matrix(d)), ncol(d))
    mCount = mConsist = matrix(c(0), ncol = n, nrow = n)
    ml[[1]] = c(0)
    for (k in 2:maxK) {
        ml[[k]] = mConsist  #initialize
    }

    if (is.null(distance))
        distance <- "euclidean"  ## necessary if d is a dist object and attr( d, 'method' ) == NULL

    acceptable.distance <- c("euclidean", "maximum", "manhattan", "canberra", "binary",
        "minkowski", "pearson", "spearman")

    main.dist.obj <- NULL
    if (diss) {
        main.dist.obj <- d
        ## reset the pFeature & weightsFeature params if they've been set (irrelevant if d
        ## is a dist matrix)
        if ((!is.null(pFeature)) && (pFeature < 1)) {
            message("user-supplied data is a distance matrix; ignoring user-specified pFeature parameter\n")
            pFeature <- 1  # set it to 1 to avoid problems with sampleCols
        }
        if (!is.null(weightsFeature)) {
            message("user-supplied data is a distance matrix; ignoring user-specified weightsFeature parameter\n")
            weightsFeature <- NULL  # set it to NULL to avoid problems with sampleCols
        }
    } else {
        ## d is a data matrix we're not sampling over the features
        if ((clusterAlg != "km") && (is.null(pFeature) || ((pFeature == 1) && is.null(weightsFeature)))) {
            ## only generate a main.dist.object IFF 1) d is a matrix, 2) we're not sampling
            ## the features, and 3) the algorithm isn't 'km'
            if (inherits(distance, "character")) {
                if (!distance %in% acceptable.distance & (class(try(get(distance),
                  silent = T)) != "function"))
                  stop("unsupported distance.")

                if (distance == "pearson" | distance == "spearman") {
                  main.dist.obj <- as.dist(1 - cor(d, method = distance, use = corUse))
                } else if (class(try(get(distance), silent = T)) == "function") {
                  main.dist.obj <- get(distance)(t(d))
                } else {
                  main.dist.obj <- dist(t(d), method = distance)
                }
                attr(main.dist.obj, "method") <- distance
            } else stop("unsupported distance specified.")
        } else {
            ## pFeature < 1 or a weightsFeature != NULL since d is a data matrix, the user
            ## wants to sample over the gene features, so main.dist.obj is left as NULL
        }
    }


    require(parallel)
    parRes <- mclapply(X = 1:repCount, FUN = function(xi) {
        eachRep(xi, d, pItem, pFeature, weightsItem, weightsFeature, main.dist.obj,
            clusterAlg, distance, innerLinkage, maxK, verbose, mConsist, ml)
    }, mc.cores = coreCount)


    for (r in 1:repCount) {
        for (k in 2:maxK) {

            ## mCount is possible number of times that two sample occur in same random sample,
            ## independent of k mCount stores number of times a sample pair was sampled
            ## together.

            mCount <- connectivityMatrix(rep(1, length(parRes[[r]][[1]][[3]])), mCount,
                parRes[[r]][[1]][[3]])

            ml[[k]] <- connectivityMatrix(parRes[[r]][[k]], ml[[k]], parRes[[r]][[1]][[3]])
        }
    }

    ## consensus fraction
    res = vector(mode = "list", maxK)
    for (k in 2:maxK) {
        ## fill in other half of matrix for tally and count.
        tmp = triangle(ml[[k]], mode = 3)
        tmpCount = triangle(mCount, mode = 3)
        res[[k]] = tmp/tmpCount
        res[[k]][which(tmpCount == 0)] = 0
    }
    message("end fraction")
    return(res)

}  # End ccRun


eachRep <- function(i, d, pItem, pFeature, weightsItem, weightsFeature, main.dist.obj,
    clusterAlg, distance, innerLinkage, maxK, verbose, mConsist, ml) {
    # for (i in 1:repCount){

    require(fastcluster)

    print(i)
    resKs <- list()

    ## take expression matrix sample, samples and genes
    sample_x = sampleCols(d, pItem, pFeature, weightsItem, weightsFeature)

    this_dist = NA
    if (!is.null(main.dist.obj)) {
        boot.cols <- sample_x$subcols
        this_dist <- as.matrix(main.dist.obj)[boot.cols, boot.cols]
        if (clusterAlg != "km") {
            ## if this isn't kmeans, then convert to a distance object
            this_dist <- as.dist(this_dist)
            attr(this_dist, "method") <- attr(main.dist.obj, "method")
        }
    } else {
        ## if main.dist.obj is NULL, then d is a data matrix, and either: 1) clusterAlg is
        ## 'km' 2) pFeatures < 1 or weightsFeatures have been specified, or 3) both so we
        ## can't use a main distance object and for every iteration, we will have to
        ## re-calculate either 1) the distance matrix (because we're also sampling the
        ## features as well), or 2) the submat (if using km)

        if (clusterAlg != "km") {
            if (!distance %in% acceptable.distance & (class(try(get(distance), silent = T)) !=
                "function"))
                stop("unsupported distance.")
            if ((class(try(get(distance), silent = T)) == "function")) {
                this_dist <- get(distance)(t(sample_x$submat))
            } else {
                if (distance == "pearson" | distance == "spearman") {
                  this_dist <- as.dist(1 - cor(sample_x$submat, use = corUse, method = distance))
                } else {
                  this_dist <- dist(t(sample_x$submat), method = distance)
                }
            }
            attr(this_dist, "method") <- distance
        } else {
            ## if we're not sampling the features, then grab the colslice
            if (is.null(pFeature) || ((pFeature == 1) && is.null(weightsFeature))) {
                this_dist <- d[, sample_x$subcols]
            } else {
                if (is.na(sample_x$submat)) {
                  stop("error submat is NA")
                }

                this_dist <- sample_x$submat
            }
        }
    }

    ## cluster samples for HC.
    this_cluster = NA
    if (clusterAlg == "hc") {
        this_cluster = fastcluster::hclust(this_dist, method = innerLinkage)
    }


    ## use samples for each k
    for (k in 2:maxK) {
        if (verbose) {
            message(paste("  k =", k))
        }
        if (i == 1) {
            ml[[k]] = mConsist  #initialize
        }
        this_assignment = NA
        if (clusterAlg == "hc") {
            ## prune to k for hc
            this_assignment = cutree(this_cluster, k)

        } else if (clusterAlg == "kmdist") {
            this_assignment = kmeans(this_dist, k, iter.max = 10, nstart = 1, algorithm = c("Hartigan-Wong"))$cluster

        } else if (clusterAlg == "km") {
            ## this_dist should now be a matrix corresponding to the result from sampleCols
            this_assignment <- kmeans(t(this_dist), k, iter.max = 10, nstart = 1,
                algorithm = c("Hartigan-Wong"))$cluster
        } else if (clusterAlg == "pam") {
            this_assignment <- pam(x = this_dist, k, diss = TRUE, metric = distance,
                cluster.only = TRUE)
        } else {
            ## optional cluterArg Hook.
            this_assignment <- get(clusterAlg)(this_dist, k)
        }
        # add to the tally was here
        resKs[[k]] <- this_assignment
    }  # End Ks
    resKs[[1]] <- sample_x
    gc()
    return(resKs)
}  # end eachRep


connectivityMatrix <- function(clusterAssignments, m, sampleKey) {
    ## input: named vector of cluster assignments, matrix to add connectivities
    ## output: connectivity matrix
    names(clusterAssignments) <- sampleKey
    cls <- lapply(unique(clusterAssignments), function(i) as.numeric(names(clusterAssignments[clusterAssignments %in% i])))  #list samples by clusterId

    for (i in 1:length(cls)) {
        nelts <- 1:ncol(m)
        cl <- as.numeric(nelts %in% cls[[i]])  ## produces a binary vector
        updt <- outer(cl, cl)  #product of arrays with * function; with above indicator (1/0) statement updates all cells to indicate the sample pair was observed int the same cluster;
        m <- m + updt
    }
    return(m)
}



sampleCols <- function(d, pSamp = NULL, pRow = NULL, weightsItem = NULL, weightsFeature = NULL) {
    ## returns a list with the sample columns, as well as the sub-matrix & sample
    ## features (if necessary) if no sampling over the features is performed, the
    ## submatrix & sample features are returned as NAs to reduce memory overhead


    space <- ifelse(inherits(d, "dist"), ncol(as.matrix(d)), ncol(d))
    sampleN <- floor(space * pSamp)
    sampCols <- sort(sample(space, sampleN, replace = FALSE, prob = weightsItem))

    this_sample <- sampRows <- NA
    if (inherits(d, "matrix")) {
        if ((!is.null(pRow)) && ((pRow < 1) || (!is.null(weightsFeature)))) {
            ## only sample the rows and generate a sub-matrix if we're sampling over the
            ## row/gene/features
            space = nrow(d)
            sampleN = floor(space * pRow)
            sampRows = sort(sample(space, sampleN, replace = FALSE, prob = weightsFeature))
            this_sample <- d[sampRows, sampCols]
            dimnames(this_sample) <- NULL
        } else {
            ## do nothing
        }
    }
    return(list(submat = this_sample, subrows = sampRows, subcols = sampCols))
}

CDF = function(ml, breaks = 100) {
    # plot CDF distribution
    plot(c(0), xlim = c(0, 1), ylim = c(0, 1), col = "white", bg = "white", xlab = "consensus index",
        ylab = "CDF", main = "consensus CDF", las = 2)
    k = length(ml)
    this_colors = rainbow(k - 1)
    areaK = c()
    for (i in 2:length(ml)) {
        v = triangle(ml[[i]], mode = 1)

        # empirical CDF distribution. default number of breaks is 100
        h = hist(v, plot = FALSE, breaks = seq(0, 1, by = 1/breaks))
        h$counts = cumsum(h$counts)/sum(h$counts)

        # calculate area under CDF curve, by histogram method.
        thisArea = 0
        for (bi in 1:(length(h$breaks) - 1)) {
            thisArea = thisArea + h$counts[bi] * (h$breaks[bi + 1] - h$breaks[bi])  #increment by height by width
            bi = bi + 1
        }
        areaK = c(areaK, thisArea)
        lines(h$mids, h$counts, col = this_colors[i - 1], lwd = 2, type = "l")
    }
    legend(0.8, 0.5, legend = paste(rep("", k - 1), seq(2, k, by = 1), sep = ""),
        fill = this_colors)

    # plot area under CDF change.
    deltaK = areaK[1]  #initial auc at k=2
    for (i in 2:(length(areaK))) {
        # proportional increase relative to prior K.
        deltaK = c(deltaK, (areaK[i] - areaK[i - 1])/areaK[i - 1])
    }
    plot(1 + (1:length(deltaK)), y = deltaK, xlab = "k", ylab = "relative change in area under CDF curve",
        main = "Delta area", type = "b")
}


myPal = function(n = 10) {
    # returns n colors
    seq = rev(seq(0, 255, by = 255/(n)))
    palRGB = cbind(seq, seq, 255)
    rgb(palRGB, maxColorValue = 255)
}

setClusterColors = function(past_ct, ct, colorU, colorList) {
    # description: sets common color of clusters between different K
    newColors = c()
    if (length(colorList) == 0) {
        # k==2
        newColors = colorU[ct]
        colori = 2
    } else {
        newColors = rep(NULL, length(ct))
        colori = colorList[[2]]
        mo = table(past_ct, ct)
        m = mo/apply(mo, 1, sum)
        for (tci in 1:ncol(m)) {
            # for each cluster
            maxC = max(m[, tci])
            pci = which(m[, tci] == maxC)
            if (sum(m[, tci] == maxC) == 1 & max(m[pci, ]) == maxC & sum(m[pci, ] ==
                maxC) == 1) {
                # if new column maximum is unique, same cell is row maximum and is also unique
                # Note: the greatest of the prior clusters' members are the greatest in a current
                # cluster's members.
                newColors[which(ct == tci)] = unique(colorList[[1]][which(past_ct ==
                  pci)])  # one value
            } else {
                # add new color.
                colori = colori + 1
                newColors[which(ct == tci)] = colorU[colori]
            }
        }
    }
    return(list(newColors, colori, unique(newColors)))
}

clusterTrackingPlot = function(m) {
    # description: plots cluster tracking plot input: m - matrix where rows are k,
    # columns are samples, and values are cluster assignments.
    plot(NULL, xlim = c(-0.1, 1), ylim = c(0, 1), axes = FALSE, xlab = "samples",
        ylab = "k", main = "tracking plot")
    for (i in 1:nrow(m)) {
        rect(xleft = seq(0, 1 - 1/ncol(m), by = 1/ncol(m)), ybottom = rep(1 - i/nrow(m),
            ncol(m)), xright = seq(1/ncol(m), 1, by = 1/ncol(m)), ytop = rep(1 -
            (i - 1)/nrow(m), ncol(m)), col = m[i, ], border = NA)
    }
    # hatch lines to indicate samples
    xl = seq(0, 1 - 1/ncol(m), by = 1/ncol(m))
    segments(xl, rep(-0.1, ncol(m)), xl, rep(0, ncol(m)), col = "black")  #** alt white and black color?
    ypos = seq(1, 0, by = -1/nrow(m)) - 1/(2 * nrow(m))
    text(x = -0.1, y = ypos[-length(ypos)], labels = seq(2, nrow(m) + 1, by = 1))
}

triangle = function(m, mode = 1) {
    # mode=1 for CDF, vector of lower triangle. mode==3 for full matrix. mode==2 for
    # calcICL; nonredundant half matrix coun mode!=1 for summary
    n = dim(m)[1]
    nm = matrix(0, ncol = n, nrow = n)
    fm = m


    nm[upper.tri(nm)] = m[upper.tri(m)]  #only upper half

    fm = t(nm) + nm
    diag(fm) = diag(m)

    nm = fm
    nm[upper.tri(nm)] = NA
    diag(nm) = NA
    vm = m[lower.tri(nm)]

    if (mode == 1) {
        return(vm)  #vector
    } else if (mode == 3) {
        return(fm)  #return full matrix
    } else if (mode == 2) {
        return(nm)  #returns lower triangle and no diagonal. no double counts.
    }

}


rankedBarPlot = function(d, myc, cc, title) {
    colors = rbind()  #each row is a barplot series
    byRank = cbind()

    spaceh = 0.1  #space between bars
    for (i in 1:ncol(d)) {
        byRank = cbind(byRank, sort(d[, i], na.last = F))
        colors = rbind(colors, order(d[, i], na.last = F))
    }
    maxH = max(c(1.5, apply(byRank, 2, sum)), na.rm = T)  #maximum height of graph

    # barplot largest to smallest so that smallest is in front.
    barp = barplot(apply(byRank, 2, sum), col = myc[colors[, 1]], space = spaceh,
        ylim = c(0, maxH), main = paste("item-consensus", title), border = NA, las = 1)
    for (i in 2:nrow(byRank)) {
        barplot(apply(matrix(byRank[i:nrow(byRank), ], ncol = ncol(byRank)), 2, sum),
            space = spaceh, col = myc[colors[, i]], ylim = c(0, maxH), add = T, border = NA,
            las = 1)
    }
    xr = seq(spaceh, ncol(d) + ncol(d) * spaceh, (ncol(d) + ncol(d) * spaceh)/ncol(d))
    # class labels as asterisks
    text("*", x = xr + 0.5, y = maxH, col = myc[cc], cex = 1.4)  #rect(xr,1.4,xr+1,1.5,col=myc[cc] )
}