[R] [lattice::xyplot] Using (panel:.)abline with panel.superpose?

[Szumiloski, John]

Dear useRs,

I recently had a query concerning how to customize the graphics parameters in lattice::xyplot to change not only the color but also the pch symbols, lty and lwd line parameters, etc., within each grouping variable in the plot.  (https://stat.ethz.ch/pipermail/r-help/2015-July/430285.html).  Many thanks to Mark Leeds who described the solution using panel.superpose as the panel function and defining a custom panel.groups function using the subscripts argument.

Here is a crude example.  Note how the pch parameter varies with grouping variable as well as color.  I have commented out two lines which are not important for the example but are for my main question.

#### begin code 1

# R version 3.2.2 release, lattice version 0.20-33, Windows 7.

    dat <- data.frame(Trt=rep(c('1','2'), each=10),
                      Sbj=rep(c('1','2'), each=5),
                      X=rep(c(0,1,2,3,4), times=4),
                      Y=c(1,3,3,3,1, 2,4,4,4,2,
                          3,1,1,1,3, 4,2,2,2,4)
                     )

    xgrid <- seq(0L, 4L)
    ygrid <- seq(0L, 5L)

    require(lattice)
    xyplot(Y ~ X | Trt, data=dat, groups=Sbj, type='b', lty=1, cex=2, lwd=3,
           scales=list(x=list(at=xgrid), y=list(at=ygrid)),
           ### abline=list(h=ygrid, v=xgrid, col=gray(0.8)),
           mycol=c('red', 'blue'), mypch=c(16,17),
           panel=panel.superpose,
           panel.groups=function(x, y, subscripts,
                                  mycol, mypch, col.line, col.symbol, pch, ...) {
                                 ### panel.abline(h=ygrid, v=xgrid, col=gray(0.8))
                                 panel.xyplot(x, y, ...,
                                                     pch = mypch[dat[['Sbj']][subscripts]],
                                              col.symbol = mycol[dat[['Sbj']][subscripts]],
                                                col.line = mycol[dat[['Sbj']][subscripts]]
                                             )
                                } # function
          ) # xyplot

### end code 1

My question involves the commented out lines.  I would like to draw a light grid in the panels.  If I used panel.grid() it would be impossible to get the gridlines into arbitrary positions, as it seems to pick values similar to pretty() (I would love to be corrected on this).  So we can use an abline argument to the main xyplot call, or a panel.abline() call in the panel.groups function.

But either way leads to a problem.  The ablines seem to be rerendered for each level of the grouping variable, thus only the final level is plotted without being the grid rendered on top of it.  Try it by uncommenting either line.

This is not totally surprising as it does mention somewhere in the documentation that panel.groups() is called for each value of the grouping variable.  So my question: How do I render the grid just once, before actually rendering the data, so as to avoid this problem?

I realized a good place to start might be to include panel.abline in the panel function itself, rather in the panel.groups function called several times per panel.  Thus something like this:

### begin code 2

    xyplot(Y~X|Trt, data=dat, groups=Sbj, type='b', lty=1, cex=2, lwd=3,
           scales=list(x=list(at=xgrid), y=list(at=ygrid)),
           mycol=c('red', 'blue'), mypch=c(16,17),
           panel=function(x, y, ...) {   ##########  <---------------- new panel function
                          panel.abline(h=ygrid, v=xgrid, col=gray(0.9))
                          panel.superpose(x, y, ...)
                         },
           panel.groups=function(x, y, subscripts,
                                  mycol, mypch, col.line, col.symbol, pch, ...) {
                                 panel.xyplot(x, y, ...,
                                                     pch = mypch[dat[['Sbj']][subscripts]],
                                              col.symbol = mycol[dat[['Sbj']][subscripts]],
                                                col.line = mycol[dat[['Sbj']][subscripts]]
                                             )
                                } # function
          ) # xyplot

### end code 2

Of course this won't work as written, I need to replace the ... arguments with the right ones.  Here is where I am having trouble.  I have tried all kinds of permutations of the mycol etc., xgrid etc., subscripts etc., and never got the plot to render the ablines once, then the data correctly.

Any assistance greatly appreciated.
John
John Szumiloski, Ph.D.
Principal Scientist, Statistician
Analytical and Bioanalytical Development
NBR105-1-1411

Bristol-Myers Squibb
P.O. Box 191
1 Squibb Drive
New Brunswick, NJ
08903-0191
USA

(732) 227-7167



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