Problems with plot and Quartz device (PR#13744)

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