Re: [Rd] Problems with plot and Quartz device (PR#13744)

From: Simon Urbanek <simon.urbanek_at_r-project.org>
Date: Wed, 03 Jun 2009 16:25:51 -0400

Thanks, Thomas.

It is indeed a very interesting phenomenon. Apparently the discrete structure in the data interacts with the way the data are plotted on a very small scale. I have committed a work-around - it forces rectangles to retain at least their original width/height when snapping to pixels causes it to shrink to 0 (i.e. the width or height is < 0.5 pixels).

Thanks,
Simon

On Jun 3, 2009, at 14:54 , Thomas Richardson wrote:

> Dear Simon,
>
> Thank you very much for the very rapid response!
>
>> rna is not defined in R, can you, please, supply a reproducible
>> example?
>
> Apologies for including code that could not be run directly.
> (I had assumed simulating "similar" data would give the same
> behaviour, but having done more experiments, I see that it is not so
> simple to get this - which makes me very curious about what is
> really going on!)
>
> I have put the data that I used on the web. I enclose R code below.
> At least on my machine a simple visual comparison of the first
> column of plots in these two quartz windows shows that half of the
> points in these plots, those on the left side of each panel, have
> disappeared in the larger quartz window!
>
> Thanks again.
>
> Best wishes,
>
> Thomas
>
> -----------------------------------------------
>
> # (Hopefully) reproducible code for disappearing pch="." points
> phenomenon
>
> mydata <- read.table("http://www.stat.washington.edu/tsr/
> streaking.dat")
>
> quartz()
> par(mfrow=c(8,12), mar=c(0,0,0,0), oma=c(0,0,0,0))
> for(i in 1:8){ # Row counter
> for(j in 1:12){ # Col counter
> xtmp <- mydata[,1]
> x <- xtmp[(mydata[,3]==i)&(mydata[,4]==j)]
> ytmp <- mydata[,2]
> y <- ytmp[(mydata[,3]==i)&(mydata[,4]==j)]
> plot
> (x,y,xaxt="n",yaxt="n",ann=FALSE,xlim=c(0,100),ylim=c(0,300),pch=".")
> }
> }
>
> quartz(width=12,height=8)
> par(mfrow=c(8,12), mar=c(0,0,0,0), oma=c(0,0,0,0))
> for(i in 1:8){ # Row counter
> for(j in 1:12){ # Col counter
> xtmp <- mydata[,1]
> x <- xtmp[(mydata[,3]==i)&(mydata[,4]==j)]
> ytmp <- mydata[,2]
> y <- ytmp[(mydata[,3]==i)&(mydata[,4]==j)]
> plot
> (x,y,xaxt="n",yaxt="n",ann=FALSE,xlim=c(0,100),ylim=c(0,300),pch=".")
> }
> }
>
>
> -----------------------------------------------
> On Wed, 3 Jun 2009, Simon Urbanek wrote:
>
>> Thomas,
>>
>
>> From your description I think I know roughly what's going on
>> (Quartz attempts to snap rectangles on pixel boundaries to prevent
>> malignant anti-aliasing effects in image plots and this may somehow
>> interact with pch='.' since Quartz has no way of knowing that those
>> rectangles are supposed to be glyphs), but I cannot reproduce it.
>>
>> Thanks,
>> Simon
>>
>>
>> On Jun 3, 2009, at 4:45 , tsr_at_stat.washington.edu wrote:
>>
>>> Full_Name: Thomas Richardson
>>> Version: R 2.9.0 GUI 1.28 Tiger build 32-bit (5395)
>>> OS: 10.4.11
>>> Submission from: (NULL) (216.254.15.72)
>>> I have encountered a problem with points in scatterplots
>>> disappearing in a
>>> quartz window when it is re-sized (to make it larger).
>>> I am constructing an 8x12 matrix of scatterplots each containing
>>> approx 600
>>> points.
>>> In order to get them in the window I remove the axes etc.,
>>> quartz()
>>> par(mfrow=c(8,12), mar=c(0,0,0,0), oma=c(0,0,0,0))
>>> for(i in 1:8){ # Row counter
>>> for(j in 1:12){ # Col counter plot(rna$red[(rna$row==levels(rna
>>> $row[i])&(rna$col==j)],
>>> rna$tof[(rna$row==levels(rna$row[i])&(rna$col==j)],
>>> xlab="tof",ylab="green",xaxt="n",yaxt="n",
>>> ann=FALSE,xlim=c(0,100),ylim=c(0,300),pch=".")
>>> }
>>> }
>>> Here is the problem: how many data points actually appear in the
>>> quartz window
>>> on my screen is highly sensitive to the width and height
>>> specified. If I specify
>>> a different width and height for the quartz window e.g.
>>> quartz(width=8,height=8), OR if I resize the window with the
>>> cursor then points
>>> disappear in certain (x-axis) ranges across all the plots in some
>>> columns. These
>>> bands in which points disappear are the same for all plots in a
>>> given column,
>>> and can be very wide - making a lot of points disappear.
>>> (The visual effect is to make it look as if there are clearly
>>> defined vertical
>>> white lines going across the scatterplots - though the black lines
>>> enclosing
>>> each plot are not broken).
>>> The problem seems to disappear with other plotting symbols e.g.
>>> pch="+" (but
>>> then I end up with crowded plots). So I guess it might be related
>>> to the
>>> "special treatment" of "." described on help(points) ??
>>> ---
>>> Value pch="." (equivalently pch = 46) is handled specially. It is
>>> a rectangle of
>>> side 0.01 inch (scaled by cex).
>>> ---
>>> I find this behaviour unnerving: the (resized) plots made it look
>>> as if there
>>> was a lot of structure in the data, but on closer inspection it
>>> turned out to be
>>> entirely a consequence of the quartz device and plot function!
>>> I can't imagine that this behaviour is intended - even if it were
>>> intended to
>>> suppress points (like some axis labels) - it seems strange that
>>> enlarging the
>>> window makes points disappear. (I also tried setting dpi=72 in
>>> quartz(), but
>>> this did not fix the problem).
>>> Thanks in advance.
>>> Thomas
>>> ------------------------------------------------------
>>> sessionInfo()
>>> R version 2.9.0 (2009-04-17)
>>> i386-apple-darwin8.11.1
>>> locale:
>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>> ______________________________________________
>>> R-devel_at_r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>



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