R/missPattern.R

In missRows: Handling Missing Individuals in Multi-Omics Data Integration

missPattern <- function(object, colStrata=NULL, colMissing="grey70",
                        cexTitles=12, legTitle="Strata",
                        missLab="miss", showPlot=TRUE) {
    
    ##- checking general input arguments -------------------------------------#
    ##------------------------------------------------------------------------#
    
    ##- object
    if (class(object) != "MIDTList") {
        stop("'object' must be an object of class 'MIDTList'.", call.=FALSE)
    }
    
    ##- colStrata
    
    ##- internal function for character color checking -----------#
    ##------------------------------------------------------------#
    isColor <- function(x) { vapply(x, function(x) {
        tryCatch(is.matrix(col2rgb(x)), error=function(e) FALSE) },
        TRUE)
    }
    ##------------------------------------------------------------#
    
    strata <- factor(colData(object)[, object@strata])
    names(strata) <- rownames(colData(object))
    
    if (is.null(colStrata)) {
        colStrata <- rainbow(length(levels(strata)))
        names(colStrata) <- levels(strata)
    } else {
        if (length(colStrata) != length(levels(strata))) {
            stop("'colStrata' must be a color names vector of length ",
                length(levels(strata)), ".", call.=FALSE)
        } else {
            if (any(!isColor(colStrata))) {
                stop("'colStrata' must be a character vector of recognized",
                    " colors.", call.=FALSE)
            }
        }
    }
    
    if (is.null(names(colStrata))) {
        names(colStrata) <- levels(strata)
    } else {
        if (any(!(names(colStrata) %in% levels(strata))))
            stop("names of 'colStrata' must be a character from: ",
                toString(levels(strata)), call.=FALSE)
    }
    
    ##- colMissing
    if (length(as.vector(colMissing)) != 1) {
        stop("'colMissing' must be a single character of recognized colors.",
            call.=FALSE)
    }
    
    if (!isColor(colMissing) | is.na(colMissing)) {
        stop("'colMissing' must be a single character of recognized colors.",
            call.=FALSE)
    }
    
    ##- end checking ---------------------------------------------------------#
    
    
    ##- initialization of variables ------------------------------------------#
    ##------------------------------------------------------------------------#
    missData <- lapply(assays(object), t)
    nmTables <- names(object)
    
    mrp <- matrix(nrow=length(strata), ncol=length(missData))
    rownames(mrp) <- names(strata)
    colnames(mrp) <- nmTables
    
    nbmr <- matrix(nrow=length(levels(strata)), ncol=length(missData))
    rownames(nbmr) <- levels(strata)
    colnames(nbmr) <- nmTables
    
    
    ##- finds the missing data pattern ---------------------------------------#
    ##------------------------------------------------------------------------#
    for (i in names(missData)) {
        id.miss <- (names(strata) %in% missingIndv(object)[[i]])
        tmp <- split(id.miss, strata)
        nbmr[, i] <- vapply(tmp, sum, 1L)
        tmp <- unlist(split(id.miss, strata))
        mrp[, i] <- tmp
    }
    
    nbmr <- rbind(nbmr, c(colSums(nbmr)))
    nbmr <- cbind(nbmr, c(rowSums(nbmr)))
    colnames(nbmr)[ncol(nbmr)] <- "    "
    mrp <- data.frame(mrp, strata = strata)
    
    ##- plot missing rows pattern --------------------------------------------#
    ##------------------------------------------------------------------------#
    ymax <- cumsum(table(mrp$strata))
    ymin <- c(0, ymax[-length(ymax)])
    
    ymin.m <- seq(0, length(strata) - 1)
    ymax.m <- seq_along(strata)
    
    df <- data.frame(ymin = NA, ymax = NA, strata = NA, Table = NA)
    df.m <- data.frame(ymin = 0, ymax = 0, strata = "", Table = nmTables[1])
    
    for (i in seq_along(missData)) {
        tmp <- data.frame(ymin = ymin, ymax = ymax, strata = levels(strata),
                            Table = rep(nmTables[i], length(levels(strata))))
        df <- rbind(df, tmp)
        
        id <- mrp[, i]
        tmp <- data.frame(ymin = ymin.m, ymax = ymax.m,
                            strata = rep(missLab, nrow(mrp)),
                            Table = rep(nmTables[i], nrow(mrp)))
        tmp <- tmp[id, ]
        df.m <- rbind(df.m, tmp)
    }
    
    df <- df[-1, ]
    df$strata <- factor(df$strata,
                        levels=c(sort(unique(df$strata)), "", missLab))
    df.m$strata <- factor(df.m$strata, levels=c("", missLab))
    df$Table <- factor(df$Table, levels=nmTables)
    df.m$Table <- factor(df.m$Table, levels=nmTables)
    
    ind.cols <- c(colStrata, "transparent", colMissing)
    names(ind.cols)[length(colStrata) + seq_len(2)] <- c("", missLab)
    
    g <- ggplot() + theme_bw() + facet_wrap(~ Table) +
        scale_y_reverse(expand=c(0, 1.5)) +
        geom_rect(data=df, aes(xmin=0, xmax=1, ymin=ymin, ymax=ymax,
                                    fill=strata), colour="white") +
        geom_rect(data=df.m, aes(xmin=0, xmax=1, ymin=ymin, 
                                    ymax=ymax, fill=strata),
                    colour="white") +
        scale_fill_manual(values=ind.cols, breaks=names(ind.cols),
                            name=legTitle) +
        theme(panel.grid.major=element_blank(),
                panel.grid.minor=element_blank(),
                axis.text=element_blank(),
                axis.ticks=element_blank(),
                strip.text=element_text(size=cexTitles)) +
        ggtitle("Missingness pattern") +
        theme(plot.title=element_text(hjust=0.5)) +
        xlab("features") + ylab("individuals")
    
    if (showPlot) { print(g) }
    
    ##- results --------------------------------------------------------------#
    ##------------------------------------------------------------------------#
    res <- list(nbMissing = nbmr, isMissing = mrp, ggp = g)
    class(res) = "missPattern"
    return(invisible(res))
}