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
??, 13 ???. 2020 ?. ? 18:56, Alexey Shipunov <dactylorhiza at
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
>
> ??, 13 ???. 2020 ?. ? 02:16, Martin Maechler <maechler at
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.sarkar at
gmail.com>:
> > >>
> > >> On Mon, Feb 17, 2020 at 10:24 AM Rui Barradas
<ruipbarradas at 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 <ruipbarradas at
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
> > >> > >>>
______________________________________________
On 2/07/20 2:58 am, Alexey Shipunov wrote:> 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.I just tried example(dotchart) and the results look fine to me. In particular the group labels are definitely visible. My session info follows.>> sessionInfo() > R version 4.0.2 (2020-06-22) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 18.04.4 LTS > > Matrix products: default > BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3 > LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3 > > Random number generation: > RNG: Mersenne-Twister > Normal: Inversion > Sample: Rounding > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_NZ.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_NZ.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=en_NZ.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] brev_0.0-4 > > loaded via a namespace (and not attached): > [1] compiler_4.0.2 tools_4.0.2<SNIP> cheers, Rolf Turner -- Honorary Research Fellow Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276
Alexey Shipunov
2020-Jul-01 23:24 UTC
[R] [FORGED] Re: Unintended behaviour (possibly bugs)
I need to clarify. This part of example(dotchart) does not show group labels in my case: == dotchart(VADeaths, main = "Death Rates in Virginia - 1940") == My session is ==> sessionInfo()R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.6 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] colorout_1.2-2 loaded via a namespace (and not attached): [1] compiler_4.0.2 tools_4.0.2 == Alexey Shipunov ??, 2 ???. 2020 ?. ? 08:18, Rolf Turner <r.turner at auckland.ac.nz>:> > > On 2/07/20 2:58 am, Alexey Shipunov wrote: > > > 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. > > I just tried example(dotchart) and the results look fine to me. In > particular the group labels are definitely visible. My session info > follows. > > >> sessionInfo() > > R version 4.0.2 (2020-06-22) > > Platform: x86_64-pc-linux-gnu (64-bit) > > Running under: Ubuntu 18.04.4 LTS > > > > Matrix products: default > > BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3 > > LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3 > > > > Random number generation: > > RNG: Mersenne-Twister > > Normal: Inversion > > Sample: Rounding > > > > locale: > > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_NZ.UTF-8 LC_COLLATE=en_GB.UTF-8 > > [5] LC_MONETARY=en_NZ.UTF-8 LC_MESSAGES=en_GB.UTF-8 > > [7] LC_PAPER=en_NZ.UTF-8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] brev_0.0-4 > > > > loaded via a namespace (and not attached): > > [1] compiler_4.0.2 tools_4.0.2 > > <SNIP> > > cheers, > > Rolf Turner > > -- > Honorary Research Fellow > Department of Statistics > University of Auckland > Phone: +64-9-373-7599 ext. 88276
>>>>> 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 > ??, 13 ???. 2020 ?. ? 18:56, Alexey Shipunov <dactylorhiza at 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 >> >> ??, 13 ???. 2020 ?. ? 02:16, Martin Maechler <maechler at 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.sarkar at gmail.com>: >> > >> >> > >> On Mon, Feb 17, 2020 at 10:24 AM Rui Barradas <ruipbarradas at 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 <ruipbarradas at 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 >> > >> > >>> ______________________________________________
Martin, Yes, I should have test it earlier. Thank you for the response! With best wishes, Alexey ??, 2 ???. 2020 ?. ? 22:30, Martin Maechler <maechler at stat.math.ethz.ch>:> > >>>>> 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 > > > ??, 13 ???. 2020 ?. ? 18:56, Alexey Shipunov <dactylorhiza at 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 > >> > >> ??, 13 ???. 2020 ?. ? 02:16, Martin Maechler <maechler at 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.sarkar at gmail.com>: > >> > >> > >> > >> On Mon, Feb 17, 2020 at 10:24 AM Rui Barradas <ruipbarradas at 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 <ruipbarradas at 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 > >> > >> > >>> ______________________________________________