Dear Deepayan and Sundar, Thank you so much for your help with this. However, I may have phrased my problem too specifically, assuming that *in general* I could apply your response to all Lattice graphics.
What I need is a barchart or vertical dotchart, with error bars, across three treatments, with a form that should look something like: barchart(median~fac1|by1, groups=group1). Your solution works great with the problem I had posed <xyplot(voice.part ~ median|by1, groups=group1, [snip]>, yet when I switch the axes for a vertical dotchart <xyplot(median~voice.part|by1, groups=group1, [snip]> the error bars remain horizontal and do not follow the switched axes. I tried to alter all 'lx' and 'ux' to 'ly' and 'uy' in panel.ci and prepanel.ci, but to no avail. I'm afraid I have not (YET) managed to understand just how Lattice works. Re. moving panel.abline() from panel.groups to panel, does that mean I need to rewrite panel.superpose? Again, any advice would be greatly appreciated. Thanks, Dan Deepayan Sarkar wrote: > On 10/12/06, Daniel E. Bunker <[EMAIL PROTECTED]> wrote: >> 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)) > > Although that does seem to be the eventual error message, this fails > not due to the lack of subscripts, but because 'panel.ci' does not > know how to deal with groups. One solution to this is Sundar's > approach, which is to change the panel function to handle groups. > Another generic solution is to use 'panel.superpose', which _does_ > know how to handle groups, and also accepts a custom panel function to > be called for each group. Often (but not always), you can use a panel > function designed for a non-groups aware display for this. In this > case, the following gives results similar to Sundar's code: > > with(singer.ucl, > xyplot(voice.part ~ median, groups=group1, > lx = lower, ux = upper, > prepanel = prepanel.ci, > panel = panel.superpose, > panel.groups = panel.ci, > pch = 16)) > > Note the need for an explicit pch=16, since the default in panel.ci is > overridden by panel.groups. > >> # what I need, ultimately, is something like this, with error bars: >> >> with(singer.ucl, >> dotplot(median~fac1|by1, groups=group1)) > > If you have more than one interval (from different groups) for any > level of your categorical variable - which seems to be the case in > this example - you will encounter a problem. The problem is this: the > grey reference lines are drawn once for every group, and will draw > over intervals drawn by calls corresponding to earlier levels. This > can be easily fixed by moving that part of the code from > 'panel.groups' to 'panel', I'll leave that as an exercise. > > -Deepayan -- Daniel E. Bunker BioMERGE Associate Director Post-Doctoral Research Scientist Columbia University Department of Ecology, Evolution and Environmental Biology 1200 Amsterdam Avenue New York, NY 10027-5557 deb37ATcolumbiaDOTedu 212-851-1888 phone 212-854-8188 fax ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
