[R] error bars in lattice xyplot *with groups*

[Deepayan Sarkar]

On 6/5/06, Mike Lawrence <Mike.Lawrence at dal.ca> wrote:
> Hi all,
>
> I'm trying to plot error bars in a lattice plot generated with xyplot. Deepayan
> Sarkar has provided a very useful solution for simple circumstances
> (https://stat.ethz.ch/pipermail/r-help/2005-October/081571.html), yet I am
> having trouble getting it to work when the "groups" setting is enabled in
> xyplot (i.e. multiple lines). To illustrate this, consider the singer data
> generated by the above linked solution previously submitted:
>
> #####################
> library(lattice)
> singer.split <-
>     with(singer,
>          split(height, voice.part))
>
> singer.ucl <-
>     sapply(singer.split,
>            function(x) {
>                st <- boxplot.stats(x)
>                c(st$stats[3], st$conf)
>            })
>
> singer.ucl <- as.data.frame(t(singer.ucl))
> names(singer.ucl) <- c("median", "lower", "upper")
> singer.ucl$voice.part <-
>     factor(rownames(singer.ucl),
>            levels = rownames(singer.ucl))
>
> #now let's split up the voice.part factor into two factors,
> singer.ucl$voice=factor(rep(c(1,2),4))
> singer.ucl$range=factor(rep(c("Bass","Tenor","Alto","Soprano"),each=2))
>
> #here's Deepayan's previous solution, slightly modified to depict
> #  the dependent variable (median) and the error bars on the y-axis
> #  and the independent variable (voice.part) on the x-axis
> prepanel.ci <- function(x, y, ly, uy, subscripts, ...)
> {
>     x <- as.numeric(x)
>     ly <- as.numeric(ly[subscripts])
>     uy <- as.numeric(uy[subscripts])
>     list(ylim = range(y, uy, ly, finite = TRUE))
> }
> panel.ci <- function(x, y, ly, uy, subscripts, pch = 16, ...)
> {
>     x <- as.numeric(x)
>     y <- as.numeric(y)
>     ly <- as.numeric(ly[subscripts])
>     uy <- as.numeric(uy[subscripts])
>     panel.arrows(x, ly, x, uy, col = "black",
>                  length = 0.25, unit = "native",
>                  angle = 90, code = 3)
>     panel.xyplot(x, y, pch = pch, ...)
> }
>
>
> #this graph works
> xyplot(median ~ voice.part,
>         data=singer.ucl,
>         ly = singer.ucl$lower,
>         uy = singer.ucl$upper,
>         prepanel = prepanel.ci,
>         panel = panel.ci,
>         type="b"
> )
>
> #this one does not (it will plot, but will not seperate the groups)
> xyplot(median ~ voice,
>         groups=range,
>         data=singer.ucl,
>         ly = singer.ucl$lower,
>         uy = singer.ucl$upper,
>         prepanel = prepanel.ci,
>         panel = panel.ci,
>         type="b"
> )
>
> ####################################
>
> Any suggestions?

Use a panel function that knows about groups, e.g.

xyplot(median ~ voice,
        groups=range,
        data=singer.ucl,
        ly = singer.ucl$lower,
        uy = singer.ucl$upper,
        prepanel = prepanel.ci,
        panel = panel.superpose,
        panel.groups = panel.ci,
        type="b")

If you prefer colored bars, change panel.ci to


panel.ci <- function(x, y, ly, uy, subscripts, pch = 16, col.line =
'black', ...)
{
    x <- as.numeric(x)
    y <- as.numeric(y)
    ly <- as.numeric(ly[subscripts])
    uy <- as.numeric(uy[subscripts])
    panel.arrows(x, ly, x, uy, col = col.line,
                 length = 0.25, unit = "native",
                 angle = 90, code = 3)
    panel.xyplot(x, y, pch = pch, col.line = col.line, ...)
}

Deepayan