Dear colleagues, There is a new problem with dotchart(), and it is very simple to reproduce.
Just run example(dotchart). On R versions < 4, group labels ("Urban Female" and so on) were visible. Now they are not visible. If in the dotchart() code, we replace the string === goffset <- (max(linch + offset, ginch, na.rm = TRUE) + 1/16)/lheight === with the string === goffset <- (max(linch + 0.2, ginch, na.rm = TRUE) + 1/16)/lheight === everything start to be OK. Probably, the reason that in the code, there is another "offset" object and they clash. So if we replace this part of code === offset <- cumsum(c(0, diff(as.numeric(groups)) != 0)) y <- seq_len(n) + 2 * offset === with === offset1 <- cumsum(c(0, diff(as.numeric(groups)) != 0)) y <- seq_len(n) + 2 * offset1 === everything will be well again. With best wishes, Alexey Shipunov пт, 13 мар. 2020 г. в 18:56, Alexey Shipunov <dactylorh...@gmail.com>: > > Dear Martin, > > Great news, thanks! > > If you wish, please also consider my initial note about help(hist), > this is definitely worrying new R users. > > With best wishes, > > Alexey > > пт, 13 мар. 2020 г. в 02:16, Martin Maechler <maech...@stat.math.ethz.ch>: > > > > >>>>> Alexey Shipunov > > >>>>> on Tue, 18 Feb 2020 14:34:48 +0900 writes: > > > > > Thank you for the detailed explanation. I tend to agree. However, this > > > behavior is relatively easy to remediate: > > > > > This is the piece of the current code: > > > > > === > > > if (!(is.null(labels) && is.null(glabels))) { > > > nmai <- par("mai") > > > nmai[2L] <- nmai[4L] + max(linch + goffset, ginch) + 0.1 > > > par(mai = nmai) > > > } > > > === > > > > > This is my proposal: > > > > > === > > > yinch <- if (!is.null(ylab)) 0.4 else 0 > > > if (!(is.null(labels) && is.null(glabels))) { > > > nmai <- par("mai") > > > nm.2 <- nmai[4L] + max(if(is.null(ylab)) 0 else 0.4) + linch + > > goffset, ginch) + 0.1 > > > if (nmai[2L] < nm.2) > > > nmai[2L] <- nm.2 > > > par(mai = nmai) > > > } > > > === > > > > > Then margins and y-axis labels start to work normally. I wonder if > > > this (or similar) is possible to introduce into the code? > > > > > Alexey > > > > Well, I had looked at this back then (~Feb 18), and now had a > > considerable longer look. > > > > Your suggestion makes sense, but then it needs even more work > > to ensure that the 'ylab' y-axis label will be placed properly. > > > > Of course, Deepayan (author of grid-based 'lattice') is right > > that dotchart()s implementation is pretty hackish ... but then > > still. > > > > I have (+-) fixed this in the sources of "R-devel" the > > development version of R (which should become R 4.0.0 on April > > 24 as was announced today). > > > > Now, things like this (extended) example work nicely : > > > > op <- par(xaxs = "i") # 0 -- 100\% > > dotchart(t(VADeaths), xlim = c(0,100), bg = "skyblue", > > main = "Death Rates in Virginia - 1940", xlab = "rate [ % ]", > > ylab = "Grouping: Age x Urbanity . Gender") > > par(op) > > > > > > Thank you, Alexey, for your report and bug fix suggestion! > > > > Best regards, > > > > Martin Maechler > > ETH Zurich and R Core team > > > > > > > > > ........... 17:37, Deepayan Sarkar <deepayan.sar...@gmail.com>: > > >> > > >> On Mon, Feb 17, 2020 at 10:24 AM Rui Barradas <ruipbarra...@sapo.pt> > > wrot= > > > e: > > >> > > > >> > Hello, > > >> > > > >> > Yes, this is definitely a bug. > > >> > > >> I would argue that the only bug here is that the documentation > > doesn't > > >> say that 'ylab' may not behave as expected. > > >> > > >> dotchart() is mainly designed for 2-way tables (see the VADeaths > > >> example), but it's implementation is really pretty hackish because it > > >> has to work within the limited traditional graphics framework. The > > >> main problem is that dot plots want to put horizontal y-axis labels > > >> (usually derived from factor levels), which are often longer than the > > >> default margins, so the margins are modified. Unfortunately they are > > >> only re-set on exit, and so the ylab that is plotted inside > > dotchart() > > >> may be clipped. Traditionally, Cleveland dot plots don't have a > > y-axis > > >> label; it's assumed that the factor levels are sufficient (and for > > >> 2-way tables, there would be two variables, so there is no sensible > > >> default). > > >> > > >> I doubt that dotchart() is worth fixing (except to maybe disallow > > >> ylab). If you want flexibility, use modern grid-based alternatives > > >> such as lattice::dotplot() or ggplot2. > > >> > > >> -Deepayan > > >> > > >> > Even the matrix plot is puzzling, with a "1" as top row > > sort-of-label > > >> > but no grid line. I'm trying to follow the source code of dotchart > > but > > >> > am yet to understand exactly what it does to decide the margins > > setting= > > > s. > > >> > > > >> > if (!(is.null(labels) && is.null(glabels))) { > > >> > nmai <- par("mai") > > >> > nmai[2L] <- nmai[4L] + max(linch + goffset, ginch) + > > >> > 0.1 > > >> > par(mai = nmai) > > >> > } > > >> > > > >> > This should be moved to r-devel? > > >> > > > >> > Rui Barradas > > >> > > > >> > 03:33 de 17/02/20, Alexey Shipunov escreveu: > > >> > > John and Rui, thanks! > > >> > > > > >> > > However, if we use the proper object, the problem still persists: > > >> > > > > >> > > dotchart(c("3"=1, "2"=2, "1"=3), ylab="Ylab") # ylab is invisible > > >> > > dotchart(c("aa"=1, "b"=2, "cc"=3), ylab="Ylab") # ylab is partly > > visible (!!!) > > >> > > dotchart(c("aaa"=1, "bbb"=2, "ccc"=3), ylab="Ylab") # ylab is > > well visible > > >> > > > > >> > > If the object is matrix, ylab is visible: > > >> > > > > >> > > dotchart(matrix(1:3, dimnames=list(c("aa","bb","cc"), NULL)), > > ylab="Ylab") > > >> > > > > >> > > But the ?dotchart explicitly says that "x: either a vector or > > matrix > > >> > > of numeric values" and then "labels: a vector of labels for each > > >> > > point. For vectors the default is to use "names(x) = ...". > > >> > > > > >> > > So this is likely a bug. Do you agree? > > >> > > > > >> > > Alexey > > >> > > > > >> > > ..... 01:55, Rui Barradas <ruipbarra...@sapo.pt>: > > >> > >> > > >> > >> Hello, > > >> > >> > > >> > >> I believe you are wrong, the error is not in dotchart, it's in > > your > > >> > >> code. You assume that to plot an object of class "table" is the > > same as > > >> > >> to plot an object of class "numeric". > > >> > >> > > >> > >> Inline. > > >> > >> > > >> > >> =C3=80s 12:21 de 16/02/20, Alexey Shipunov escreveu: > > >> > >>> Dear list, > > >> > >>> > > >> > >>> I have been advised to share these with R-help instead of > > filling the > > >> > >>> bug report: > > >> > >>> > > >> > >>> 1) dotchart() does not allow to see the left axis title > > ('ylab') and > > >> > >>> cannot change the left margin (outer margin 2) of the plot > > >> > >>> > > >> > >>> The code: > > >> > >>> > > >> > >>> aa <- table(c(1, 1, 1, 2, 2, 3)) > > >> > >>> dotchart(aa, ylab="Ylab") # does not show 'ylab' > > >> > >> > > >> > >> You are right, it does *not* show 'ylab' but the user is warned. > > >> > >> > > >> > >> > > >> > >> aa <- table(c(1, 1, 1, 2, 2, 3)) > > >> > >> dotchart(aa, ylab = "Ylab") # does show 'ylab' > > >> > >> #Warning message: > > >> > >> #In dotchart(aa, ylab = "Ylab") : > > >> > >> # 'x' is neither a vector nor a matrix: using as.numeric(x) > > >> > >> > > >> > >> > > >> > >> My code: > > >> > >> > > >> > >> > > >> > >> (mar <- par("mar")) # new R session > > >> > >> #[1] 5.1 4.1 4.1 2.1 # the left margin is 4.1 > > >> > >> > > >> > >> aa <- as.numeric(table(c(1, 1, 1, 2, 2, 3))) > > >> > >> > > >> > >> dotchart(aa, ylab = "Ylab") # It does show 'ylab' > > >> > >> old.par <- par(mar = mar + c(0, 5, 0, 0)) > > >> > >> par("mar") > > >> > >> #[1] 5.1 9.1 4.1 2.1 > > >> > >> > > >> > >> dotchart(aa, ylab = "Ylab") # The left margin is now 9.1, much > > bigger > > >> > >> > > >> > >> par(old.par) # It does change the left margin > > >> > >> dotchart(aa, ylab = "Ylab") # but only when a new graph is > > plotted. > > >> > >> > > >> > >> > > >> > >> > > >> > >>> old.par <- par(mar=c(1, 10, 1, 1)) ; dotchart(aa, ylab="Ylab") > > ; > > >> > >>> par(old.par) # does not change left margin > > >> > >>> > > >> > >>> Possible solution: > > >> > >>> > > >> > >>> I researched the problem and think that the dotchart() code > > will need > > >> > >>> few corrections. If there is an interest, I can post it here; > > or you > > >> > >>> can look at the code of shipunov::Dotchart1() function. > > >> > >>> > > >> > >>> 2) example(hist) includes two "wrong" and "extreme" examples > > which > > >> > >>> slow down and even crash R on some systems; this make it > > unsuitable > > >> > >>> for demonstration in the class and strikes beginners in R who > > just > > >> > >>> want to understand how hist() works. Actually, I did it last > > week (I > > >> > >>> was not aware of these examples), and in the class two > > computers hang, > > >> > >>> and many others were extremely slow. > > >> > >>> > > >> > >>> The code: > > >> > >>> > > >> > >>> example(hist) > > >> > >>> > > >> > >>> Possible solution: > > >> > >>> > > >> > >>> If R maintainers will enclose parts of "hist" example in > > \dontrun{}, > > >> > >>> this will allow to see the code but in the same time will not > > strike > > >> > >>> beginners in R who just > > >> > >>> want to understand how hist() works. They will still be > > possible to > > >> > >>> run with example(..., run.dontrun=TRUE). > > >> > >> > > >> > >> Agree, it's annoying. Sometimes there's a Warning section after > > the > > >> > >> Details section. Maybe such a section could get users' > > attention to > > >> > >> those examples? At least it wouldn't hurt... > > >> > >> > > >> > >> > > >> > >> Hope this helps, > > >> > >> > > >> > >> Rui Barradas > > >> > >> > > >> > >>> > > >> > >>> With best wishes, > > >> > >>> > > >> > >>> Alexey Shipunov > > >> > >>> ______________________________________________ ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.