>>>>> Alexey Shipunov >>>>> on Wed, 1 Jul 2020 23:58:04 +0900 writes:
> 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. Thank you. I'll have a look *again*, and cautiously consider the above. Indeed your second patch seems the correct one, distinguishing the two different offsets that where conflated. I will commit to R-devel and also to "R 4.0.2 patched" (but note that no quick R 4.0.3 has been planned). Note (Alexey knows, almost everbody else probably not): This has come from another dotchart(* , ylab=.) glitch which Alexey had reported in February and I had fixed early March... evidently not fixed quite correctly... and yes, I'm embarrased. However I did mention here to have fixed it, on March 12 (--> https://stat.ethz.ch/pipermail/r-help/2020-March/465921.html ) It would have been really great if people would test such changes, as they were in all pre-releases (R 4.0.0 alpha, beta, RC), easily available ... and we could have fixed this even before R 4.0.0 was released more than a month later than my e-mail above... Martin > 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.