qqthin: a version of qqplot() that thins out points that overplot

In hddplot: Use Known Groups in High-Dimensional Data to Derive Scores for Plots

a version of qqplot() that thins out points that overplot

Description

QQ-plots with large numbers of points typically generate graphics files that are unhelpfully large. This function handles the problem by removing points that are, for all practical purposes, redundant

Usage

qqthin(x, y, ends = c(0.01, 0.99), eps = 0.001, xlab = deparse(substitute(x)),
       adj.xlab = NULL, ylab = deparse(substitute(y)), show.line = TRUE,
       print.thinning.details=TRUE, centerline = TRUE, ...)

Arguments

x	ordered values of x will be plotted on the x-axis
y	ordered values of y will be plotted on the y-axis
ends	outside these cumulative proportions of numbers of points, all points will be included in the graph
eps	controls the extent of overplotting
xlab	label for x-axis
adj.xlab	positioning of x-label
ylab	label for y-axis
show.line	logical; show the line y=x?
print.thinning.details	logical; print number of points after thinning?
centerline	logical; draw a line though the part of the graph where some points have been omitted?
...	additional graphics parameters

Value

Gives a qqplot. The number of points retained is returned invisibly.

Author(s)

John Maindonald

References

~put references to the literature/web site here ~

Examples

mat <- matrix(rnorm(1000), ncol=20)
cl <- factor(rep(1:3, c(7,9,4)))
Fstats <- aovFbyrow(x = mat, cl = cl)
qqthin(qf(ppoints(length(Fstats)), 2, 17), Fstats, eps=0.01)


## The function is currently defined as
function(x, y, ends=c(.01,.99), eps=0.001,
           xlab = deparse(substitute(x)), adj.xlab=NULL,
           ylab = deparse(substitute(y)), show.line=TRUE,
           print.thinning.details=TRUE,
           centerline=TRUE, ...){
    ## qqthin() is a substitute for qqplot(), that thins
    ## out plotted points from the region where they are
    ## dense.  Apart from the overlaid curve that shows
    ## the region where points have been thinned, it may
    ## be hard to distinguish the result of qqthin()
    ## from that of qqplot()
    xlab <- xlab
    ylab <- ylab
    x <- sort(x)
    y <- sort(y)
    dx<-diff(x)
    epsdist <- sqrt(diff(range(x))^2+diff(range(y))^2)*eps
    dx<-0.5*(c(dx[1],dx)+c(dx,dx[length(dx)]))
    dy<-diff(y)
    dy<-0.5*(c(dy[1],dy)+c(dy,dy[length(dy)]))
    dpoints <- epsdist/sqrt(dx^2+dy^2)
    ## dpoints is a local measure of the number of points
    ## per unit distance along the diagonal, with the unit
    ## set to approximately eps*(length of diagonal)
    dig<-floor(dpoints)+1
    ## dig is, roughly, the number of points per unit distance.
    ## We wish to retain one point per unit distance.  For this
    ## retain points where cdig rounds to an integer. For such
    ## points, cdig has increased by approx 1, relative to the
    ## previous point that is retained.
    cdig<-round(cumsum(1/dig))
    subs<-match(unique(cdig), cdig)
    if(is.null(adj.xlab))
    plot(x[subs], y[subs], xlab=xlab, ylab=ylab)
    else {
      plot(x[subs], y[subs], xlab="", ylab=ylab)
      mtext(side=1, xlab, adj=adj.xlab, line=par()$mgp[1])
    }
    if(any(diff(subs)>1)){
    n1 <- min(subs[c(diff(subs),0)>1])
    n2 <- max(subs[c(0,diff(subs))>1])
    ns1 <- match(n1, subs)
    ns2 <- match(n2, subs)
    if(print.thinning.details)
       print(paste("Graph retains", length(subs), "points."))
    if(centerline)
      lines(smooth.spline(x[subs[ns1:ns2]], y[subs[ns1:ns2]]),
            col="grey", lwd=2)
	    }
    if(show.line)abline(0, 1, col="red")
invisible(length(subs))
  }

hddplot documentation built on Sept. 14, 2023, 5:07 p.m.