Thanks Thierry, I didn't know about that, it's always nice to see different ways of doing things. Question: How would you add the bars ?
Hope to see more interesting replies, Tal On Wed, Aug 12, 2009 at 1:29 PM, ONKELINX, Thierry <thierry.onkel...@inbo.be > wrote: > This can be done much easier and transparent with ggplot2 > > library(ggplot2) > ggplot(mtcars, aes(x = factor(round(wt)), y = mpg, colour = factor(am))) > + geom_boxplot() + geom_point(stat = "summary", fun.y = "mean", position > = position_dodge(width = 0.75)) > > HTH, > > Thierry > > ------------------------------------------------------------------------ > ---- > ir. Thierry Onkelinx > Instituut voor natuur- en bosonderzoek / Research Institute for Nature > and Forest > Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, > methodology and quality assurance > Gaverstraat 4 > 9500 Geraardsbergen > Belgium > tel. + 32 54/436 185 > thierry.onkel...@inbo.be > www.inbo.be > > To call in the statistician after the experiment is done may be no more > than asking him to perform a post-mortem examination: he may be able to > say what the experiment died of. > ~ Sir Ronald Aylmer Fisher > > The plural of anecdote is not data. > ~ Roger Brinner > > The combination of some data and an aching desire for an answer does not > ensure that a reasonable answer can be extracted from a given body of > data. > ~ John Tukey > > -----Oorspronkelijk bericht----- > Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > Namens Tal Galili > Verzonden: woensdag 12 augustus 2009 11:48 > Aan: r-help@r-project.org > Onderwerp: [R] A function for plotting a boxplot with added dot and bars > (formean and SE) - please help improve my code > > Hello people, > > A while back I wanted to plot boxplots with interactions that will have > a dot for the mean of the sample + bars for the SE. > After searching for some code, I found something that did it for one > level, but couldn't find something that will allow for interactions the > way the original boxplot does. > > After playing with the original code, I found a way for allowing the > boxplot code to introduce interactions to it. The price for that was > that I was forced to use a little different syntax for the function then > that of the original boxplot. In order to use the function, one must use > lists for the function input arguments, and until now I didn't find a > way for doing the same task from a formula input. > So for example, the original boxplot will be written like this: > boxplot(y ~ A*B) > Where as my function will look like this: > boxplot.2(y , list(A,B) ) > > > > In this e-mail I am giving away the code for: > 1) helping out others searching for this solution. and > 2) in hope to have more experienced R programmers come by and improve on > this code (by, for example, removing the for loop in it, or allowing to > use a formula instead of a list input) > > > > Here is the code: > > > boxplot.2 <- function(fo.head, list.fo.tail = list(1), print.mean = T, > plot.CI = T, add.mean.sd.to.boxplot.names = T, plot.round.factor = 2 > ,...) { > require(gplots) > tmp <- split(fo.head , list.fo.tail) > means <- sapply(tmp, mean) > stdev <- sqrt(sapply(tmp, var)) #IS right - because of the sqrt !!! > <- sqrt(sapply(tmp, var)) # was var, I changed it to sd > n <- sapply(tmp,length) > ciw <- qt(0.975, n-1) * stdev / sqrt(n) > old.names = attributes(tmp)$names > length.of.names = length(old.names) > new.names = as.list(old.names) > for(i in c(1:length.of.names)) > { > new.names[[i]] <- paste(old.names[i], " (", > round(means[i],plot.round.factor) ,",", round(ciw[i],plot.round.factor) > ,")", sep = "") > } > > if(add.mean.sd.to.boxplot.names) > { > if(length(list.fo.tail) == 1) > { > sub.text = paste("mean:", round(means,3), > "(SE:",round(ciw,3), " ; N:" ,n, ")") > boxplot(tmp, xlab = sub.text, cex.axis = min(1, > mean(c(1,12/ > max(nchar(new.names)) )) ), ...) > } else { > boxplot(tmp, names = new.names, cex.axis = min(1, > mean(c(1,12/ > max(nchar(new.names)) )) ), ...) > } > } else { boxplot(tmp, ...) } # else - make boxplot without them > > # adding the points and the bars > points(means, col = 'red', pch = 19) > if(require(gplots) & plot.CI) { > plotCI(x=means, uiw=ciw, col="white", barcol="blue", > xaxt="n" , add = T) > } > > if(print.mean) { > small.mean.and.se.table <- rbind(round(means,3),round(ciw,3), n) > rownames(small.mean.and.se.table) <- c("means:", "SE's:", "N") > print(t(small.mean.and.se.table)) > } > } # <-- end boxplot3 > > > # Here is a small example: > data(mtcars) > head(mtcars) > attach(mtcars) > boxplot.2(mpg , list(round(wt), am) , data = mtcars, las = 2) > > > > > > > Hope this will benefit others, and also hope that others will improve on > this code and give it back to the community, Tal galili > > > > -- > ---------------------------------------------- > > > My contact information: > Tal Galili > Phone number: 972-50-3373767 > FaceBook: Tal Galili > My Blogs: > http://www.r-statistics.com/ > http://www.talgalili.com > http://www.biostatistics.co.il > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org 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. > > Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver > weer > en binden het INBO onder geen enkel beding, zolang dit bericht niet > bevestigd is > door een geldig ondertekend document. The views expressed in this message > and any annex are purely those of the writer and may not be regarded as > stating > an official position of INBO, as long as the message is not confirmed by a > duly > signed document. > -- ---------------------------------------------- My contact information: Tal Galili Phone number: 972-50-3373767 FaceBook: Tal Galili My Blogs: http://www.r-statistics.com/ http://www.talgalili.com http://www.biostatistics.co.il [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org 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.
