Since points() and lines() plot on the scale of the last plot, you could plot
your "first" graph after the "second" one, or if there is a particular reason
why you plot them in the order you do, add a third, empty graph with the scale
of the first one as the last plot.
B.
On 2014-05-07, at 2:37 PM, Dustin Fife wrote:
> Hi,
>
> In my work, I often investigate relationships between highly skewed data.
> Example:
>
> set.seed(111)
> require(MASS)
> d = data.frame(mvrnorm(1000, mu=c(0,0), Sigma=matrix(c(1,.6,.6,1), nrow=2)))
> names(d) = c("x","y")
> ## Skew Y
> d$y = d$y^4
> plot(d$x, d$y)
> lines(lowess(d$x, d$y), lwd=2, col="blue")
>
> Unfortunately, with such skewed data, it's hard to see the line unless we
> "zoom in," by either ignoring the outliers, or "breaking" the scale of the
> y axis, such that the first 2/3 of the graph correspond to a "normal"
> scale, and the remaining 1/3 correspond to a "compressed" scale. (I know
> this is generally not recommended, see
> http://r.789695.n4.nabble.com/split-a-y-axis-to-show-data-on-different-scales-td805816.html).
> I created a function to do this:
>
> scaleBreak = function(x,y,axis=2, breakpos=1,...){
>
> #### figure out which Y values are above the breakpos
> y_above = y[y>breakpos]; x_above = x[y>breakpos]
> y_below = y[y<=breakpos]; x_below = x[y<=breakpos]
>
> #### pick ranges
> range_1 = range(y_below)
> range_2 = range(y_above)
>
> #### find limits of y axis (so it spans 2/3rds)
> mx = max(y_below); mn = min(y_below)
> ylims1 = c(mn, mx + (mx-mn)/2)
>
> #### plot bottom graph
> plot(range(x), ylims1, type="n", yaxt="n",...)
> points(x_below, y_below, yaxt="n",...)
> axis(2, pretty(y_below))
>
> min2 = (breakpos + .45*breakpos - max(y))/.45
>
> #### add second graph
> par(new=TRUE)
> plot(range(x), c(min2, max(y)), type="n", yaxt="n", xaxt="n", ylab="",
> axes=F)
> points(x_above, y_above, yaxt="n",...)
> axis(2, pretty(y_above)[-1])
> require(plotrix)
> axis.break(axis=axis, breakpos)
>
> }
>
> The problem I'm having is that the fitted line is not printed on the scale
> of the bottom 2/3 plot:
>
> scaleBreak(d$x, d$y, breakpos=20)
> lines(lowess(d$x, d$y), lwd=2, col="blue")
>
> Can anyone think of a solution where the line is on the scale of the bottom
> 2/3 of the plot, in the right location? (Again, let me preempt the
> objections others might raise about how this should not be done. I know it
> generally should not be done, but let's pretend I have an excellent reason
> :) )
>
> Thanks in advance!
>
> [[alternative HTML version deleted]]
>
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