[R] adding error bars to lattice plots

[Sundar Dorai-Raj]

Daniel E. Bunker said the following on 10/12/2006 11:48 AM:
> Dear R users,
> 
> About a year ago Deepayan offered a suggestion to incorporate error bars 
> into a dotplot using the singer data as an example 
> <<http://finzi.psych.upenn.edu/R/Rhelp02a/archive/63875.html>>.
> 
> When I try to utilize this code with a grouping variable, I get an error 
> stating that the subscripts argument is missing.  I have tried to insert 
> them in various ways, but cannot figure out where they should go.
> 
> Deepayan's original code follows, with additions from me for factor, 
> grouping and by variables.
> 
> (Note that I could use xYplot (Dotplot), but I need my response variable 
> on the vertical axis.)
> 
> Any suggestions would be greatly appreciated.
> 
> Thanks, Dan
> 
> prepanel.ci <- function(x, y, lx, ux, subscripts, ...) {
>         x <- as.numeric(x)
>         lx <- as.numeric(lx[subscripts])
>          ux <- as.numeric(ux[subscripts])
>          list(xlim = range(x, ux, lx, finite = TRUE))
>      }
> 
> panel.ci <- function(x, y, lx, ux, subscripts, pch = 16, ...) {
>          x <- as.numeric(x)
>          y <- as.numeric(y)
>          lx <- as.numeric(lx[subscripts])
>          ux <- as.numeric(ux[subscripts])
>          panel.abline(h = unique(y), col = "grey")
>          panel.arrows(lx, y, ux, y, col = 'black',
>                   length = 0.25, unit = "native",
>                   angle = 90, code = 3)
>          panel.xyplot(x, y, pch = pch, ...)
>      }
> 
> 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$voice.part <-
>      factor(rownames(singer.ucl),
>             levels = rownames(singer.ucl))
> 
> # add factor, grouping and by variables
> singer.ucl$fac1=c("level1","level1", "level2", "level2")
> singer.ucl$by1=c("two","one")
> singer.ucl$group1=c(rep(letters[1],4),rep(letters[2],4))
> 
> ## show the data frame
> singer.ucl
> 
> # Deepayan's original example
> with(singer.ucl,
>       xyplot(voice.part ~ median,
>              lx = lower, ux = upper,
>              prepanel = prepanel.ci,
>              panel = panel.ci),
>          horizontal=FALSE)
> 
> # with by variable, works fine
> with(singer.ucl,
>       xyplot(voice.part ~ median|by1,
>              lx = lower, ux = upper,
>              prepanel = prepanel.ci,
>              panel = panel.ci))
> 
> # with groups, fails for lack of subscripts.
> with(singer.ucl,
>       xyplot(voice.part ~ median, groups=group1,
>              lx = lower, ux = upper,
>              prepanel = prepanel.ci,
>              panel = panel.ci))
> 
> 
> # what I need, ultimately, is something like this, with error bars:
> 
> with(singer.ucl,
>       dotplot(median~fac1|by1, groups=group1))
> 
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Hi, Daniel,

Try this panel function:

panel.ci <- function(x, y, lx, ux, subscripts,
                      groups = NULL, pch = 16, ...) {
   x <- as.numeric(x)
   y <- as.numeric(y)
   lx <- as.numeric(lx[subscripts])
   ux <- as.numeric(ux[subscripts])
   par <- if(is.null(groups))"plot.symbol" else "superpose.symbol"
   sym <- trellis.par.get(par)
   col <- sym$col
   groups <- if(!is.null(groups)) {
     groups[subscripts]
   } else {
     rep(1, along = x)
   }
   ug <- unique(groups)
   for(i in seq(along = ug)) {
     subg <- groups == ug[i]
     y.g <- y[subg]
     x.g <- x[subg]
     lx.g <- lx[subg]
     ux.g <- ux[subg]
     panel.abline(h = unique(y.g), col = "grey")
     panel.arrows(lx.g, y.g, ux.g, y.g, col = 'black',
                  length = 0.25, unit = "native",
                  angle = 90, code = 3)
     panel.xyplot(x.g, y.g, pch = pch, col = col[i], ...)
   }
}