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
> > >> > >>> ______________________________________________
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