[R] issues with gap.plot function

[Ben Bolker]

Zheng Lu <zlu <at> umich.edu> writes:

> 
> 
> Dear all: 
> 
> I have the following codes: 
> 
>  Xdata<-c(2,3,8,9,10)
> Ydata<-1:5
> gap.plot(Xdata, Ydata,gap=c(5,6),gap.axis="x",type="o") 
> 
> However, the type='o' seems only work on the first part of gap plot, the
second half of the plot always just
> points, you can not add lines on that part, any help will be highly
appreciated.  I would like to have these
> two parts of the plot either both are points or both are lines or both are
overlaid of lines and points. Thank
> you very much.
> 
> Zheng 

 Xdata<-c(2,3,8,9,10)
Ydata<-1:5
gap.plot(Xdata, Ydata,gap=c(5,6),gap.axis="x",type="o")

  You can fix this problem by changing the function so that
every instance of points() has a ... at the end -- for
example:

my.gap.plot <-
function (x, y, gap, gap.axis = "y", xticlab, xtics = NA, yticlab,
    ytics = NA, col = rep(par("col"), length(x)), xlim, ylim,
    pch = rep(1, length(x)), ...)
{
    if (missing(y) && !missing(x)) {
        y <- x
        x <- 1:length(y)
    }
    if (missing(gap))
        stop("gap must be specified")
    gapsize <- diff(gap)
    if (missing(xtics))
        xtics <- pretty(x)
    if (missing(ytics))
        ytics <- pretty(y)
    if (missing(xticlab))
        xticlab <- xtics
    if (missing(yticlab))
        yticlab <- ytics
    if (length(col) < length(y))
        col <- rep(col, length.out = length(y))
    if (gap.axis == "y") {
        littleones <- which(y <= gap[1])
        if (length(gapsize) > 2) {
            middleones <- which(y >= gap[2] & y <= gap[3])
            bigones <- which(y >= gap[4])
            lostones <- sum(c(y > gap[1] & y < gap[2], y > gap[3] &
                y < gap[4]))
            if (missing(ylim))
                ylim <- c(min(y), max(y) - (gapsize[1] + gapsize[3]))
        }
        else {
            middleones <- NA
            bigones <- which(y >= gap[2])
            lostones <- sum(y > gap[1] & y < gap[2])
            if (missing(ylim))
                ylim <- c(min(y), max(y) - gapsize[1])
        }
        if (lostones)
            warning("some values of y will not be displayed")
        if (missing(xlim))
            xlim <- range(x)
    }
    else {
        littleones <- which(x <= gap[1])
        if (length(gapsize) > 2) {
            middleones <- which(x >= gap[2] & x <= gap[3])
            bigones <- which(x >= gap[4])
            lostones <- sum(c(x > gap[1] & x < gap[2], x > gap[3] &
                x < gap[4]))
            if (missing(xlim))
                xlim <- c(min(x), max(x) - (gapsize[1] + gapsize[3]))
        }
        else {
            middleones <- NA
            bigones <- which(x >= gap[2])
            lostones <- sum(x > gap[1] & x < gap[2])
            if (missing(xlim))
                xlim <- c(min(x), max(x) - gapsize[1])
        }
        if (lostones)
            warning("some values of x will not be displayed")
        if (missing(ylim))
            ylim <- range(y)
    }
    if (length(pch) < length(x))
        pch <- rep(pch, length.out = length(x))
    plot(x[littleones], y[littleones], xlim = xlim, ylim = ylim,
        axes = FALSE, col = col[littleones], pch = pch[littleones],
        ...)
    box()
    if (gap.axis == "y") {
        if (!is.na(xtics[1]))
            axis(1, at = xtics, labels = xticlab)
        littletics <- which(ytics < gap[1])
        if (length(gapsize) > 2) {
            middletics <- which(ytics >= gap[2] & ytics <= gap[3])
            bigtics <- which(ytics >= gap[4])
            show.at <- c(ytics[littletics], ytics[middletics] -
                gapsize[1], ytics[bigtics] - (gapsize[1] + gapsize[3]))
            show.labels <- c(yticlab[littletics], yticlab[middletics],
                yticlab[bigtics])
        }
        else {
            bigtics <- which(ytics >= gap[2])
            show.at <- c(ytics[littletics], ytics[bigtics] -
                gapsize[1])
            show.labels <- c(ytics[littletics], yticlab[bigtics])
        }
        axis(2, at = show.at, labels = show.labels)
        axis.break(2, gap[1], style = "gap")
        if (length(gapsize) > 2) {
            axis.break(2, gap[3] - gapsize[1], style = "gap")
            points(x[middleones], y[middleones] - gapsize[1],
                col = col[middleones], pch = pch[middleones],...)
            points(x[bigones], y[bigones] - (gapsize[1] + gapsize[3]),
                col = col[bigones], pch = pch[bigones],...)
        }
        else points(x[bigones], y[bigones] - gapsize[1], col = col[bigones],
            pch = pch[bigones],...)
    }
    else {
        if (!is.na(ytics[1]))
            axis(2, at = ytics, labels = yticlab)
        littletics <- which(xtics < gap[1])
        if (length(gapsize) > 2) {
            middletics <- which(xtics >= gap[2] & xtics <= gap[3])
            bigtics <- which(xtics >= gap[4])
            show.at <- c(xtics[littletics], xtics[middletics] -
                gapsize[1], xtics[bigtics] - (gapsize[1] + gapsize[3]))
            show.labels <- c(xticlab[littletics], xticlab[middletics],
                xticlab[bigtics])
        }
        else {
            bigtics <- which(xtics >= gap[2])
            show.at <- c(xtics[littletics], xtics[bigtics] -
                gapsize[1])
            show.labels <- c(xticlab[littletics], xticlab[bigtics])
        }
        axis(1, at = show.at, labels = show.labels)
        axis.break(1, gap[1], style = "gap")
        if (length(gapsize) > 2) {
            axis.break(1, gap[3] - gapsize[1], style = "gap")
            points(x[middleones] - gapsize[1], y[middleones],
                col = col[middleones], pch = pch[middleones],...)
            points(x[bigones] - (gapsize[1] + gapsize[3]), y[bigones],
                col = col[bigones], pch = pch[bigones],...)
        }
        else points(x[bigones] - gapsize[1], y[bigones], col = col[bigones],
            pch = pch[bigones],...)
    }
}

my.gap.plot(Xdata, Ydata,gap=c(5,6),gap.axis="x",type="o")