[R] abline and plot(augPred) help

[Gabor Grothendieck]

On 9/4/06, Paul Murrell <p.murrell at auckland.ac.nz> wrote:
> Hi
>
>
> Petr Pikal wrote:
> > Dear all
> >
> > as I did not get any response on my post about abline and
> > plot(augPred)) I try again. I hope I do not break some posting guide
> > rules. I would try to contact package maintainer directly but there
> > is stated to be R-core people, so I feel R-help list shall be OK.
> >
> > I need to draw straight lines through augPred plotted panels
> > (vertical or horizontal) at specified point. I know I shall probably
> > use panel.abline but I am missing correct syntax. Below you can see
> > my attempts together with results. I hope somebody can point me to
> > right direction.
> >
> > I am probably somewhere close but I have no clue, which parameter I
> > shall modify to get measured points, fitted lines and vertical lines
> > in panels together.
>
>
> The problem is that you do not know about the default panel function
> that nlme:::plot.augPred() uses, so your panel functions are not
> replicating all of the default behaviour as well as adding your vertical
> lines.  Some possible solutons suggested below ...
>
>
> > fm1 <- lme(Orthodont)
> >
> > # standard plot
> > plot(augPred(fm1, level = 0:1, length.out = 2))
> >
> > #plot with vertical but without points and fitted lines
> > plot(augPred(fm1, level = 0:1, length.out = 2),
> > panel=function(v,...) {
> > panel.abline(v=10)}
> > )
> >
> > # plot with vertical but without fitted lines
> > plot(augPred(fm1, level = 0:1, length.out=2),
> > panel=function(x,y,...) {
> > panel.xyplot(x,y,...)
> > panel.abline(v=10)}
> > )
> >
> > # plot with vertical and with all points (fitted lines are drawn as
> > points)
> > plot(augPred(fm1, level = 0:1),
> > panel=function(x,y,...) {
> > panel.xyplot(x,y,...)
> > panel.abline(v=10)}
> > )
>
> One option is to take a sneak a peek at nlme:::plot.augPred() to see
> what the default panel function is doing.  Here I have replicated the
> default panel function and added a call to panel.abline().
>
> plot(augPred(fm1, level = 0:1, length.out = 2),
>  panel=function(x, y, subscripts, groups, ...) {
>                orig <- groups[subscripts] == "original"
>                panel.xyplot(x[orig], y[orig], ...)
>                panel.superpose(x[!orig], y[!orig], subscripts[!orig],
>                                groups, ..., type = "l")
>                panel.abline(v=10)
>  })
>
> The problem with this approach is that you need to crawl around in the
> code of nlme:::plot.augPred().  An alternative approach is to annotate
> the plot after-the-fact.  This is shown below.
>
> plot(augPred(fm1, level = 0:1, length.out = 2))
> for (i in 1:5) {
>  for (j in 1:6) {
>    if (i < 5 || j < 4) {
>      trellis.focus("panel", j, i, highlight=FALSE)
>      panel.abline(v=10)
>    }
>  }
> }
>
> This avoids crawling around in code, but the problem with this is
> knowing how many rows and columns of panels there are.  If you
> explicitly controlled the 'layout' of the original plot, you could
> guarantee that your annotation works properly.
>

You can find that out with trellis.currentLayout:

tcL <- trellis.currentLayout()
for(i in 1:nrow(tcL))
  for(j in 1:ncol(tcL))
    if (tcL[i,j] > 0) {
        trellis.focus("panel", j, i, highlight = FALSE)
        panel.abline(v = 10)
        trellis.unfocus()
    }