VIM: Visualization and Imputation of Missing Values

Documented in barMiss

# ---------------------------------------
# Author: Andreas Alfons ,Bernd Prantner
#         and Daniel Schopfhauser
#         Vienna University of Technology
# ---------------------------------------



#' Barplot with information about missing/imputed values
#' 
#' Barplot with highlighting of missing/imputed values in other variables by
#' splitting each bar into two parts.  Additionally, information about
#' missing/imputed values in the variable of interest is shown on the right
#' hand side.
#' 
#' If more than one variable is supplied, the bars for the variable of interest
#' are split according to missingness/number of imputed missings in the
#' additional variables.
#' 
#' If `only.miss=TRUE`, the missing/imputed values in the variable of
#' interest are visualized by one bar on the right hand side.  If additional
#' variables are supplied, this bar is again split into two parts according to
#' missingness/number of imputed missings in the additional variables.
#' 
#' Otherwise, a small barplot consisting of two bars is drawn on the right hand
#' side.  The first bar corresponds to observed values in the variable of
#' interest and the second bar to missing/imputed values.  Since these two bars
#' are not on the same scale as the main barplot, a second y-axis is plotted on
#' the right (if `axes=TRUE`).  Each of the two bars are again split into
#' two parts according to missingness/number of imputed missings in the
#' additional variables.  Note that this display does not make sense if only
#' one variable is supplied, therefore `only.miss` is ignored in that
#' case.
#' 
#' If `interactive=TRUE`, clicking in the left margin of the plot results
#' in switching to the previous variable and clicking in the right margin
#' results in switching to the next variable.  Clicking anywhere else on the
#' graphics device quits the interactive session.  When switching to a
#' continuous variable, a histogram is plotted rather than a barplot.
#' 
#' @param x a vector, matrix or `data.frame`.
#' @param delimiter a character-vector to distinguish between variables and
#' imputation-indices for imputed variables (therefore, `x` needs to have
#' [colnames()]). If given, it is used to determine the corresponding
#' imputation-index for any imputed variable (a logical-vector indicating which
#' values of the variable have been imputed). If such imputation-indices are
#' found, they are used for highlighting and the colors are adjusted according
#' to the given colors for imputed variables (see `col`).
#' @param pos a numeric value giving the index of the variable of interest.
#' Additional variables in `x` are used for highlighting.
#' @param selection the selection method for highlighting missing/imputed
#' values in multiple additional variables.  Possible values are `"any"`
#' (highlighting of missing/imputed values in *any* of the additional
#' variables) and `"all"` (highlighting of missing/imputed values in
#' *all* of the additional variables).
#' @param col a vector of length six giving the colors to be used. If only one
#' color is supplied, the bars are transparent and the supplied color is used
#' for highlighting missing/imputed values.  Else if two colors are supplied,
#' they are recycled.
#' @param border the color to be used for the border of the bars.  Use
#' `border=NA` to omit borders.
#' @param main,sub main and sub title.
#' @param xlab,ylab axis labels.
#' @param axes a logical indicating whether axes should be drawn on the plot.
#' @param labels either a logical indicating whether labels should be plotted
#' below each bar, or a character vector giving the labels.
#' @param only.miss logical; if `TRUE`, the missing/imputed values in the
#' variable of interest are visualized by a single bar.  Otherwise, a small
#' barplot is drawn on the right hand side (see \sQuote{Details}).
#' @param miss.labels either a logical indicating whether label(s) should be
#' plotted below the bar(s) on the right hand side, or a character string or
#' vector giving the label(s) (see \sQuote{Details}).
#' @param interactive a logical indicating whether variables can be switched
#' interactively (see \sQuote{Details}).
#' @param \dots further graphical parameters to be passed to
#' [graphics::title()] and [graphics::axis()].
#' @return a numeric vector giving the coordinates of the midpoints of the
#' bars.
#' @note Some of the argument names and positions have changed with version 1.3
#' due to extended functionality and for more consistency with other plot
#' functions in `VIM`.  For back compatibility, the arguments
#' `axisnames`, `names.arg` and `names.miss` can still be
#' supplied to \code{\dots{}} and are handled correctly.  Nevertheless, they
#' are deprecated and no longer documented.  Use `labels` and
#' `miss.labels` instead.
#' @author Andreas Alfons, modifications to show imputed values by Bernd
#' Prantner
#' @seealso [spineMiss()], [histMiss()]
#' @references M. Templ, A. Alfons, P. Filzmoser (2012) Exploring incomplete
#' data using visualization tools.  *Journal of Advances in Data Analysis
#' and Classification*, Online first. DOI: 10.1007/s11634-011-0102-y.
#' @keywords hplot
#' @family plotting functions
#' @examples
#' 
#' data(sleep, package = "VIM")
#' ## for missing values
#' x <- sleep[, c("Exp", "Sleep")]
#' barMiss(x)
#' barMiss(x, only.miss = FALSE)
#' 
#' ## for imputed values
#' x_IMPUTED  <- kNN(sleep[, c("Exp", "Sleep")])
#' barMiss(x_IMPUTED, delimiter = "_imp")
#' barMiss(x_IMPUTED, delimiter = "_imp", only.miss = FALSE)
#' 
#' 
#' @export
barMiss <- function(x, delimiter = NULL, pos = 1, selection = c("any","all"), 
                    col = c("skyblue","red","skyblue4","red4","orange","orange4"), 
                    border = NULL, main = NULL, sub = NULL, 
                    xlab = NULL, ylab = NULL, axes = TRUE, 
                    labels = axes, only.miss = TRUE, 
                    miss.labels = axes, interactive = TRUE, ...) {
  check_data(x)
  x <- as.data.frame(x)
  imputed <- FALSE # indicates if there are Variables with missing-index
    # initializations and error messages
    if(is.null(dim(x))) {  # vector
		# call histMiss if the plot variable is continuous
		if(is.continuous(x)) {
			histMiss(x, delimiter=delimiter, pos=pos, selection=selection, col=col, 
					border=border, main=main, sub=sub, xlab=xlab, ylab=ylab,
					axes=axes, only.miss=only.miss, 
					miss.labels=miss.labels, interactive=interactive, ...)
			return(invisible(1))
		}
        n <- length(x)
        p <- 1
        if(n == 0) stop("'x' must have positive length")
    } else {  # matrix or data.frame
        if(!(inherits(x, c("data.frame","matrix")))) { 
            stop("'x' must be a data.frame or matrix")
        }
		# call histMiss if the plot variable is continuous
		if(is.continuous(x[, pos])) {
			histMiss(x, delimiter=delimiter, pos=pos, selection=selection, col=col, 
					border=border, main=main, sub=sub, xlab=xlab, ylab=ylab,
					axes=axes, only.miss=only.miss, 
					miss.labels=miss.labels, interactive=interactive, ...)
			return(invisible(1))
		}
		## delimiter ##
		if(!is.null(delimiter)) {
			tmp <- grep(delimiter, colnames(x)) # Position of the missing-index
			if(length(tmp) > 0) {
				imp_var <- x[, tmp, drop=FALSE]
				x <- x[, -tmp, drop=FALSE]
				
				if(ncol(x) == 0) stop("Only the missing-index is given")
				if(is.matrix(imp_var) && range(imp_var) == c(0,1)) imp_var <- apply(imp_var,2,as.logical)
				
				if(is.null(dim(imp_var))) {
					if(!is.logical(imp_var)) stop("The missing-index of imputed Variables must be of the type logical")
				} else {
					if(!any(as.logical(lapply(imp_var,is.logical)))) stop("The missing-index of imputed Variables must be of the type logical")	
				}
				imputed <- TRUE
			} else {
				warning("'delimiter' is given, but no missing-index-Variable is found", call. = FALSE)
			}
		}

        n <- nrow(x)
        p <- ncol(x)
        if(n == 0) stop("'x' has no rows")
        else if(p == 0) stop("'x' has no columns")
        if(is.null(colnames(x))) colnames(x) <- defaultNames(p)
    }
    if(p == 1) {
        only.miss <- TRUE
        interactive <- FALSE
    } else {
       if((!is.numeric(pos)) || (length(pos) != 1) || (p < pos)) {
			stop("'pos' must be an integer specifying one column of 'x' and must be lesser than the number of colums of 'x'")
		}
        selection <- match.arg(selection)
    }

	if(length(col) == 0) col <- c("skyblue","red","skyblue4","red4","orange","orange4")
	else if(length(col) == 1) col <- c(rep.int(c("transparent", col), 2),rep.int(col,2))
	else if(length(col) == 3 || length(col) == 5) col <- rep.int(col[1:2], 3)
	else if(length(col) != 6) col <- rep(col, length.out=6)
    localAxis <- function(..., names.arg, axisnames, cex.names, names.miss) {
        axis(...)
    }
    localTitle <- function(..., names.arg, axisnames, cex.names, names.miss) {
        title(...)
    }
    
    # back compatibility
    dots <- list(...)
    nmdots <- names(dots)
    has.axisnames <- "axisnames" %in% nmdots
    if(missing(labels)) {
        if(has.axisnames) {
            if(dots$axisnames) {
                if("names.arg" %in% nmdots) labels <- dots$names.arg
                else labels <- TRUE
            } else labels <- FALSE
        } else if("names.arg" %in% nmdots) labels <- dots$names.arg
    }
    if(missing(miss.labels)) {
        if(has.axisnames) {
            if(dots$axisnames) {
                if("names.miss" %in% nmdots) miss.labels <- dots$names.miss
                else miss.labels <- TRUE
            } else miss.labels <- FALSE
        } else if("names.miss" %in% nmdots) miss.labels <- dots$names.miss
    }
    
    # workhorse to create plot
    createPlot <- function(main=NULL, sub=NULL, 
            xlab=NULL, ylab=NULL, labels=axes) {
        # prepare data
        if(is.null(dim(x))) xpos <- as.factor(x)
        else if(p == 1) {
            xpos <- as.factor(x[,1])
            if(is.null(xlab)) xlab <- colnames(x)  # default x-axis label
        } else {
            xpos <- as.factor(x[, pos])  # plot variable
            xh <- x[, -pos, drop=FALSE]  # highlight variables
            if(is.null(xlab)) xlab <- colnames(x)[pos]  # default x-axis label
        }
		
		if(p == 2 && is.null(ylab)) {  # default y-axis label
			if(!imputed) ylab <- paste("missing/observed in", colnames(x)[-pos])
			else ylab <- paste("imputed/observed in", colnames(x)[-pos])
		}
		
        # plot annotation
        x.axis <- TRUE
        if(is.logical(labels)) {
            if(!is.na(labels) && labels) labels <- NULL
            else x.axis <- FALSE
        }
        miss.axis <- TRUE
        if(is.logical(miss.labels)) {
            if(!is.na(miss.labels) && miss.labels) miss.labels <- NULL
            else miss.axis <- FALSE
        }
        
		impp <- FALSE # indicates if the current variable has imputed missings
		# get missings/imputed missings and plot limits
		if(!imputed) { # barMiss
			misspos <- isNA(xpos)
		} else { # barImp
			tmp <- isImp(x, pos = pos, delimiter = delimiter, imp_var = imp_var, selection = selection)
			misspos <- tmp[["misspos"]]
			impp <- tmp[["impp"]]
			missh <- tmp[["missh"]]
		}
		missposf <- factor(ifelse(misspos, 1, 0), levels=0:1)
		
   
		if(p == 1) ct <- table(missposf)[2]  # number of missings
		else {
			if(!imputed) missh <- isNA(xh, selection) # barMiss
			
			misshf <- factor(ifelse(missh, 1, 0), levels=1:0)
			ct <- table(misshf, missposf)  # contingency table for missings
			ct[2,] <- ct[1,] + ct[2,]  # y-coordinates for rectangles
			if(only.miss) ct <- ct[,2]
		}
	
		allNA <- all(misspos)
    	if(allNA) {
		n <- 5
        counts <- 0
		} else {
            n <- length(levels(xpos))
			counts <- summary(xpos[!misspos])
        }
        # extend x-axis limits
        br <- c(0.2, n*1.2)
        h <- br[2] - br[1]
        if(only.miss) {
            xlim <- c(br[1], br[2]+1+0.08*h)
            ylim <- c(0, max(summary(xpos)))
        } else {
            xlim <- c(br[1], br[2]+0.155*h)
            ylim <- c(0, max(counts))
        }
        if(allNA) {
            b <- NULL
            labels <- character()
            plot(xlim, ylim, type="n", ann=FALSE, axes=FALSE, yaxs="i")
            if(only.miss && axes) localAxis(side=2, ...)  # y-axis
        } else {
#            if(p > 1 && any(missh)) {
#                # missings in highlight variables: stacked barplot
#                counts <- table(missh, xpos)
#                b <- barplot(counts, col=col[2:1], border=border, 
#                    main="", sub="", xlab="", ylab="", xlim=xlim, 
#                    ylim=ylim, axes=FALSE, axisnames=FALSE)
#            } else {  # simple barplot
#                b <- barplot(counts, col=col[1], border=border, 
#                    main="", sub="", xlab="", ylab="", xlim=xlim, 
#                    ylim=ylim, axes=FALSE, axisnames=FALSE)
#            }
            b <- barplot(counts, col=col[1], border=border, 
                main="", sub="", xlab="", ylab="", xlim=xlim, 
                ylim=ylim, axes=FALSE, axisnames=FALSE)
            if(p > 1 && any(missh)) {  # add barplot for missings
                if(imputed) color <- col[5]
				else color <- col[2]
				indices <- which(is.na(x[,2]) & missh ==TRUE)
				missh2 <- missh
				missh2[-indices] <- FALSE
				countsmiss <- table(xpos[missh], useNA="no")
				countsmiss2 <- table(xpos[missh2], useNA="no")
          b <- barplot(countsmiss, col=color, border=border, 
                    add=TRUE, axes=FALSE, axisnames=FALSE)
                
          if(length(indices) > 0 & imputed) {
            b <- barplot(countsmiss2, col=col[2], border=border, 
                         add=TRUE, axes=FALSE, axisnames=FALSE)
          }
            }
			else if(p == 1 && impp == TRUE && any(misspos)) {
				countsmiss <- table(xpos[missh], useNA="no")
                b <- barplot(countsmiss, col=col[5], border=border, 
                    add=TRUE, axes=FALSE, axisnames=FALSE)
				
			}
            if(x.axis) {
                if(is.null(labels)) labels <- levels(xpos)
                else labels <- rep(labels, length.out=length(levels(xpos)))
            }
            if(axes) localAxis(side=2, ...)  # y-axis
        }
        localTitle(main, sub, xlab, ylab, ...)  # plot annotation
        abline(v=br[2]+0.04*h, col="lightgrey")
        
        # additional information about missings
        if(only.miss) {  # one bar for missings in first variable
            xleft <- br[2] + 0.08*h
            xright <- xlim[2]
            if(p == 1) {
                rect(xleft, 0, xright, ct, col=col[3], border=border, xpd=TRUE)
            } else {
				if(!imputed) color <- col[4:3]
				else color <- col[c(6,3)]
                rect(rep(xleft, 2), c(0, ct[1]), rep(xright, 2), ct, 
                    col=color, border=border, xpd=TRUE)
            }
            if(miss.axis) {
                miss.at <- xleft+(xright-xleft)/2
                if(is.null(miss.labels)) {
					if(!imputed) miss.labels <- "missing"
					else miss.labels <- "imputed"
				}
                else miss.labels <- rep(miss.labels, length.out=1)
				
            }
        } else {  # stacked barplot for observed/missing in first variable
            usr <- par("usr")
            par(usr=c(usr[1:2], 0, max(ct[2,])))  # modify user coordinates
            on.exit(par(usr=usr))  # reset user coordinates on exit
            zero <- br[2]+0.08*h
            xleft <- zero + c(0,0,1.5,1.5)*0.03*h
            ybottom <- c(0,ct[1,1],0,ct[1,2])
            xright <- zero + c(1,1,2.5,2.5)*0.03*h
            ytop <- ct
			if(!imputed) color <- col[c(2,1,4,3)]
			else color <- col[c(5,1,6,3)]
            ########################################################
            
            rect(xleft, ybottom, xright, ytop, 
                col=color, border=border, xpd=TRUE)
            ## still missings
            if(length(indices) > 0 & imputed) {
              sum_miss <- length(indices)
              xleft1 <- xleft[1]
              ybottom1 <- ybottom[1]
              xright1 <- xright[1]
              ytop1 <- sum_miss
              color1 <- col[2]
              rect(xleft1,ybottom1,xright1,ytop1,col=color1,border=border,xpd=TRUE)
            }
            ########################################################
            if(miss.axis) {
                miss.at <- zero + c(0.5,2)*0.03*h
                if(is.null(miss.labels)) {
					if(!imputed) miss.labels <- c("observed","missing")
					else miss.labels <- c("observed","imputed")
				}
                else miss.labels <- rep(miss.labels, length.out=2)
            }
            if(axes) localAxis(side=4, ...)
        }
        
        # x-axis
        if(x.axis || miss.axis) {
            x.axes <- TRUE
            dots$side <- 1
            dots$at <- c(if(x.axis) b, if(miss.axis) miss.at)
            dots$labels <- c(if(x.axis) labels, if(miss.axis) miss.labels)
            if(is.null(dots$line)) dots$line <- par("mgp")[3]
            dots$lty <- 0
            if(is.null(dots$las)) dots$las <- 3
            if(dots$las %in% 2:3) {
                space.vert <- (par("oma")[1]+par("mar")[1]-
                        dots$line-par("mgp")[2])*par("csi")
                ok <- prettyLabels(dots$labels, 
                    dots$at, space.vert, dots$cex.axis)
                if(any(ok)) {
                    dots$at <- dots$at[ok]
                    dots$labels <- dots$labels[ok]
                } else x.axes <- FALSE
            }
            if(x.axes) do.call(localAxis, dots)
        }
        
        return(b)
    }
    b <- createPlot(main, sub, xlab, ylab, labels)

    # interactive features
    interactiveDevices <- c("X11cairo","quartz","windows")
    dev <- names(dev.cur())
	
    if(interactive && any(!is.na(charmatch(interactiveDevices, dev)))) {
        cat(paste("\nClick in in the left margin to switch to the previous",
                "variable or in the right margin to switch to the next",
                "variable.\n"))
        cat(paste("To regain use of the VIM GUI and the R console,",
                "click anywhere else in the graphics window.\n\n"))
        usr <- par("usr")
        pt <- locatorVIM()
        while(!is.null(pt) && (pt$x < usr[1] || pt$x > usr[2])) {
            if(pt$x < usr[1]) pos <- if(pos == 1) p else (pos - 1) %% p
            else pos <- if(pos == p-1) p else (pos + 1) %% p
            #b <- createPlot()
            b <- 
                if(is.continuous(x[, pos])) {
                    histMiss(if(imputed) cbind(x,imp_var) else x, delimiter = delimiter, pos=pos, selection=selection, col=col, 
                        border=border, axes=axes, only.miss=only.miss, 
                        miss.labels=miss.labels, interactive=FALSE, ...)
				} else createPlot(labels=if(is.logical(labels)) labels else axes)
            usr <- par("usr")
            pt <- locatorVIM()
        }
    }
    
    invisible(b)
}